Server crashes "Exception in server tick loop"

Okay so last night my server crashed and everyone who was online lost a bit of personal data, for example, all my achievements were removed, and experience. We have essentials, and everyone who was online lost all home's they had set (those who weren't online seem to have no lost data). We also have grief prevention, and everyone's claims were set to admin claims. So everyone is locked out of their bases until I manually delete the claim and let them re-claim it. I have no idea what could have affected the files in this way, so any help is appreciated.

There was no crash report generated for the crash last night, it doesn't exist, which is odd enough. But There was another crash today, a few moments ago. It crashed, I logged back on and it crashed again, and once more after that and generated 5 crash reports. The latest one is in the spoiler below, they all have the same description, so I'm not sure if you want all of them or if one will do.

Please help me figure out what is going on, and what could be causing these crashes. Let me know if you need anymore information.

PLUGNS: Essentials, worldEdit, firstjoinplus, permissionsEx, griefprevention, Dynmap (added after first crash from last night) ExtendedChat(doesn't work), BuyCraft, WorldEditSelectionVisualizer (doesn't work)

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---- Minecraft Crash Report ----
// Don't be sad. I'll do better next time, I promise!

Time: 3/9/15 7:17 PM
Description: Exception in server tick loop

java.lang.IllegalArgumentException: ChunkNibbleArrays should be 2048 bytes not: 0
at net.minecraft.server.v1_8_R1.NibbleArray.<init>(NibbleArray.java:14)
at net.minecraft.server.v1_8_R1.ChunkRegionLoader.a(ChunkRegionLoader.java:385)
at net.minecraft.server.v1_8_R1.ChunkRegionLoader.a(ChunkRegionLoader.java:97)
at net.minecraft.server.v1_8_R1.ChunkRegionLoader.loadChunk(ChunkRegionLoader.java:86)
at org.bukkit.craftbukkit.v1_8_R1.chunkio.ChunkIOProvider.callStage1(ChunkIOProvider.java:19)
at org.bukkit.craftbukkit.v1_8_R1.chunkio.ChunkIOProvider.callStage1(ChunkIOProvider.java:1)
at org.bukkit.craftbukkit.v1_8_R1.util.AsynchronousExecutor$Task.init(AsynchronousExecutor.java:150)
at org.bukkit.craftbukkit.v1_8_R1.util.AsynchronousExecutor$Task.initAsync(AsynchronousExecutor.java:95)
at org.bukkit.craftbukkit.v1_8_R1.util.AsynchronousExecutor$Task.run(AsynchronousExecutor.java:85)
at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)
at java.lang.Thread.run(Unknown Source)


A detailed walkthrough of the error, its code path and all known details is as follows:
---------------------------------------------------------------------------------------

-- System Details --
Details:
Minecraft Version: 1.8
Operating System: Linux (amd64) version 3.14.32-xxxx-grs-ipv6-64
Java Version: 1.7.0_75, Oracle Corporation
Java VM Version: Java HotSpot(TM) 64-Bit Server VM (mixed mode), Oracle Corporation
Memory: 2699679416 bytes (2574 MB) / 3087007744 bytes (2944 MB) up to 3087007744 bytes (2944 MB)
JVM Flags: 2 total; -Xmx3072M -Xms3072M
IntCache: cache: 0, tcache: 0, allocated: 12, tallocated: 94
CraftBukkit Information:
Running: CraftBukkit version git-Spigot-35348a5-ee6d0fa (MC: 1.8) (Implementing API version 1.8-R0.1-SNAPSHOT) true
Plugins: { WorldEdit v6.0-beta-01;3335-e7a18b26 com.sk89q.worldedit.bukkit.WorldEditPlugin [], FirstJoinPlus v2.2 com.chaseoes.firstjoinplus.FirstJoinPlus [chaseoes], PermissionsEx v1.23.1 ru.tehkode.permissions.bukkit.PermissionsEx [[t3hk0d3, zml]], GriefPrevention v10.7.1 me.ryanhamshire.GriefPrevention.GriefPrevention [], dynmap v2.1-SNAPSHOT-1077 org.dynmap.bukkit.DynmapPlugin [mikeprimm], ExtendedChat v1.0.0 com.gmail.codervortex.ExtendedChat.Main [Vortex], Essentials vTeamCity com.earth2me.essentials.Essentials [Zenexer, ementalo, Aelux, Brettflan, KimKandor, snowleo, ceulemans, Xeology, KHobbits, md_5, Iaccidentally], Buycraft v6.7 net.buycraft.Plugin [Tebex Limited], WorldEditSelectionVisualizer v1.3.3 com.rojel.wesv.WorldEditSelectionVisualizer [Rojetto],}
Warnings: DEFAULT
Reload Count: 0
Threads: { TIMED_WAITING Snooper Timer: [java.lang.Object.wait(Native Method), java.util.TimerThread.mainLoop(Unknown Source), java.util.TimerThread.run(Unknown Source)], RUNNABLE DestroyJavaVM: [], TIMED_WAITING Craft Scheduler Thread - 1: [sun.misc.Unsafe.park(Native Method), java.util.concurrent.locks.LockSupport.parkNanos(Unknown Source), java.util.concurrent.SynchronousQueue$TransferStack.awaitFulfill(Unknown Source), java.util.concurrent.SynchronousQueue$TransferStack.transfer(Unknown Source), java.util.concurrent.SynchronousQueue.poll(Unknown Source), java.util.concurrent.ThreadPoolExecutor.getTask(Unknown Source), java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source), java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source), java.lang.Thread.run(Unknown Source)], TIMED_WAITING Craft Scheduler Thread - 3: [sun.misc.Unsafe.park(Native Method), java.util.concurrent.locks.LockSupport.parkNanos(Unknown Source), java.util.concurrent.SynchronousQueue$TransferStack.awaitFulfill(Unknown Source), java.util.concurrent.SynchronousQueue$TransferStack.transfer(Unknown Source), java.util.concurrent.SynchronousQueue.poll(Unknown Source), java.util.concurrent.ThreadPoolExecutor.getTask(Unknown Source), java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source), java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source), java.lang.Thread.run(Unknown Source)], RUNNABLE Server console handler: [java.io.FileInputStream.readBytes(Native Method), java.io.FileInputStream.read(Unknown Source), java.io.BufferedInputStream.fill(Unknown Source), java.io.BufferedInputStream.read(Unknown Source), org.bukkit.craftbukkit.libs.jline.internal.NonBlockingInputStream.read(NonBlockingInputStream.java:248), org.bukkit.craftbukkit.libs.jline.internal.InputStreamReader.read(InputStreamReader.java:261), org.bukkit.craftbukkit.libs.jline.internal.InputStreamReader.read(InputStreamReader.java:198), org.bukkit.craftbukkit.libs.jline.console.ConsoleReader.readCharacter(ConsoleReader.java:2145), org.bukkit.craftbukkit.libs.jline.console.ConsoleReader.readLineSimple(ConsoleReader.java:3183), org.bukkit.craftbukkit.libs.jline.console.ConsoleReader.readLine(ConsoleReader.java:2333), org.bukkit.craftbukkit.libs.jline.console.ConsoleReader.readLine(ConsoleReader.java:2269), org.bukkit.craftbukkit.libs.jline.console.ConsoleReader.readLine(ConsoleReader.java:2257), net.minecraft.server.v1_8_R1.ThreadCommandReader.run(ThreadCommandReader.java:35)], TIMED_WAITING Timer-0: [java.lang.Object.wait(Native Method), java.util.TimerThread.mainLoop(Unknown Source), java.util.TimerThread.run(Unknown Source)], TIMED_WAITING Thread-11: [java.lang.Thread.sleep(Native Method), org.dynmap.AsynchronousQueue.sleep(AsynchronousQueue.java:148), org.dynmap.AsynchronousQueue.running(AsynchronousQueue.java:136), org.dynmap.AsynchronousQueue.access$000(AsynchronousQueue.java:9), org.dynmap.AsynchronousQueue$1.run(AsynchronousQueue.java:83), java.lang.Thread.run(Unknown Source)], WAITING pool-14-thread-1: [sun.misc.Unsafe.park(Native Method), java.util.concurrent.locks.LockSupport.park(Unknown Source), java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject.await(Unknown Source), java.util.concurrent.LinkedBlockingQueue.take(Unknown Source), java.util.concurrent.ThreadPoolExecutor.getTask(Unknown Source), java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source), java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source), java.lang.Thread.run(Unknown Source)], TIMED_WAITING Craft Scheduler Thread - 6: [sun.misc.Unsafe.park(Native Method), java.util.concurrent.locks.LockSupport.parkNanos(Unknown Source), java.util.concurrent.SynchronousQueue$TransferStack.awaitFulfill(Unknown Source), java.util.concurrent.SynchronousQueue$TransferStack.transfer(Unknown Source), java.util.concurrent.SynchronousQueue.poll(Unknown Source), java.util.concurrent.ThreadPoolExecutor.getTask(Unknown Source), java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source), java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source), java.lang.Thread.run(Unknown Source)], RUNNABLE pool-11-thread-1 Selector0: [sun.nio.ch.EPollArrayWrapper.epollWait(Native Method), sun.nio.ch.EPollArrayWrapper.poll(Unknown Source), sun.nio.ch.EPollSelectorImpl.doSelect(Unknown Source), sun.nio.ch.SelectorImpl.lockAndDoSelect(Unknown Source), sun.nio.ch.SelectorImpl.select(Unknown Source), org.dynmap.jetty.io.nio.SelectorManager$SelectSet.doSelect(SelectorManager.java:569), org.dynmap.jetty.io.nio.SelectorManager$1.run(SelectorManager.java:290), java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source), java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source), java.lang.Thread.run(Unknown Source)], TIMED_WAITING Spigot Metrics Thread: [java.lang.Object.wait(Native Method), java.util.TimerThread.mainLoop(Unknown Source), java.util.TimerThread.run(Unknown Source)], TIMED_WAITING HashSessionScavenger-0: [java.lang.Object.wait(Native Method), java.util.TimerThread.mainLoop(Unknown Source), java.util.TimerThread.run(Unknown Source)], TIMED_WAITING Spigot Watchdog Thread: [java.lang.Thread.sleep(Native Method), org.spigotmc.WatchdogThread.run(WatchdogThread.java:92)], TIMED_WAITING File IO Thread: [java.lang.Thread.sleep(Native Method), net.minecraft.server.v1_8_R1.FileIOThread.c(SourceFile:44), net.minecraft.server.v1_8_R1.FileIOThread.run(SourceFile:30), java.lang.Thread.run(Unknown Source)], TIMED_WAITING Craft Scheduler Thread - 0: [sun.misc.Unsafe.park(Native Method), java.util.concurrent.locks.LockSupport.parkNanos(Unknown Source), java.util.concurrent.SynchronousQueue$TransferStack.awaitFulfill(Unknown Source), java.util.concurrent.SynchronousQueue$TransferStack.transfer(Unknown Source), java.util.concurrent.SynchronousQueue.poll(Unknown Source), java.util.concurrent.ThreadPoolExecutor.getTask(Unknown Source), java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source), java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source), java.lang.Thread.run(Unknown Source)], TIMED_WAITING pool-11-thread-5: [sun.misc.Unsafe.park(Native Method), java.util.concurrent.locks.LockSupport.parkNanos(Unknown Source), java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject.awaitNanos(Unknown Source), java.util.concurrent.LinkedBlockingQueue.poll(Unknown Source), java.util.concurrent.ThreadPoolExecutor.getTask(Unknown Source), java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source), java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source), java.lang.Thread.run(Unknown Source)], TIMED_WAITING Craft Scheduler Thread - 5: [sun.misc.Unsafe.park(Native Method), java.util.concurrent.locks.LockSupport.parkNanos(Unknown Source), java.util.concurrent.SynchronousQueue$TransferStack.awaitFulfill(Unknown Source), java.util.concurrent.SynchronousQueue$TransferStack.transfer(Unknown Source), java.util.concurrent.SynchronousQueue.poll(Unknown Source), java.util.concurrent.ThreadPoolExecutor.getTask(Unknown Source), java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source), java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source), java.lang.Thread.run(Unknown Source)], WAITING Craft Scheduler Thread - 2: [java.lang.Object.wait(Native Method), java.lang.Thread.join(Unknown Source), java.lang.Thread.join(Unknown Source), ru.tehkode.libs.net.gravitydevelopment.updater.Updater.waitForThread(Updater.java:354), ru.tehkode.libs.net.gravitydevelopment.updater.Updater.getResult(Updater.java:295), ru.tehkode.permissions.bukkit.PermissionsEx$2.run(PermissionsEx.java:263), org.bukkit.craftbukkit.v1_8_R1.scheduler.CraftTask.run(CraftTask.java:71), org.bukkit.craftbukkit.v1_8_R1.scheduler.CraftAsyncTask.run(CraftAsyncTask.java:53), java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source), java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source), java.lang.Thread.run(Unknown Source)], WAITING Thread-4: [sun.misc.Unsafe.park(Native Method), java.util.concurrent.locks.LockSupport.park(Unknown Source), java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject.await(Unknown Source), java.util.concurrent.LinkedBlockingQueue.take(Unknown Source), com.mojang.util.QueueLogAppender.getNextLogEvent(QueueLogAppender.java:77), org.bukkit.craftbukkit.v1_8_R1.util.TerminalConsoleWriterThread.run(TerminalConsoleWriterThread.java:25), java.lang.Thread.run(Unknown Source)], WAITING Java2D Disposer: [java.lang.Object.wait(Native Method), java.lang.ref.ReferenceQueue.remove(Unknown Source), java.lang.ref.ReferenceQueue.remove(Unknown Source), sun.java2d.Disposer.run(Unknown Source), java.lang.Thread.run(Unknown Source)], TIMED_WAITING pool-11-thread-3: [sun.misc.Unsafe.park(Native Method), java.util.concurrent.locks.LockSupport.parkNanos(Unknown Source), java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject.awaitNanos(Unknown Source), java.util.concurrent.LinkedBlockingQueue.poll(Unknown Source), java.util.concurrent.ThreadPoolExecutor.getTask(Unknown Source), java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source), java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source), java.lang.Thread.run(Unknown Source)], RUNNABLE Signal Dispatcher: [], WAITING Reference Handler: [java.lang.Object.wait(Native Method), java.lang.Object.wait(Object.java:503), java.lang.ref.Reference$ReferenceHandler.run(Unknown Source)], TIMED_WAITING Dynmap Render Thread: [sun.misc.Unsafe.park(Native Method), java.util.concurrent.locks.LockSupport.parkNanos(Unknown Source), java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject.awaitNanos(Unknown Source), java.util.concurrent.ScheduledThreadPoolExecutor$DelayedWorkQueue.take(Unknown Source), java.util.concurrent.ScheduledThreadPoolExecutor$DelayedWorkQueue.take(Unknown Source), java.util.concurrent.ThreadPoolExecutor.getTask(Unknown Source), java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source), java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source), java.lang.Thread.run(Unknown Source)], TIMED_WAITING Server Infinisleeper: [java.lang.Thread.sleep(Native Method), net.minecraft.server.v1_8_R1.ThreadSleepForever.run(SourceFile:64)], WAITING Chunk I/O Executor Thread-1: [sun.misc.Unsafe.park(Native Method), java.util.concurrent.locks.LockSupport.park(Unknown Source), java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject.await(Unknown Source), java.util.concurrent.LinkedBlockingQueue.take(Unknown Source), java.util.concurrent.ThreadPoolExecutor.getTask(Unknown Source), java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source), java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source), java.lang.Thread.run(Unknown Source)], TIMED_WAITING process reaper: [sun.misc.Unsafe.park(Native Method), java.util.concurrent.locks.LockSupport.parkNanos(Unknown Source), java.util.concurrent.SynchronousQueue$TransferStack.awaitFulfill(Unknown Source), java.util.concurrent.SynchronousQueue$TransferStack.transfer(Unknown Source), java.util.concurrent.SynchronousQueue.poll(Unknown Source), java.util.concurrent.ThreadPoolExecutor.getTask(Unknown Source), java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source), java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source), java.lang.Thread.run(Unknown Source)], TIMED_WAITING Keep-Alive-Timer: [java.lang.Thread.sleep(Native Method), sun.net.www.http.KeepAliveCache.run(Unknown Source), java.lang.Thread.run(Unknown Source)], WAITING pool-14-thread-2: [sun.misc.Unsafe.park(Native Method), java.util.concurrent.locks.LockSupport.park(Unknown Source), java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject.await(Unknown Source), java.util.concurrent.LinkedBlockingQueue.take(Unknown Source), java.util.concurrent.ThreadPoolExecutor.getTask(Unknown Source), java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source), java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source), java.lang.Thread.run(Unknown Source)], TIMED_WAITING pool-11-thread-4: [sun.misc.Unsafe.park(Native Method), java.util.concurrent.locks.LockSupport.parkNanos(Unknown Source), java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject.awaitNanos(Unknown Source), java.util.concurrent.LinkedBlockingQueue.poll(Unknown Source), java.util.concurrent.ThreadPoolExecutor.getTask(Unknown Source), java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source), java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source), java.lang.Thread.run(Unknown Source)], RUNNABLE Netty Server IO #1: [sun.nio.ch.EPollArrayWrapper.epollWait(Native Method), sun.nio.ch.EPollArrayWrapper.poll(Unknown Source), sun.nio.ch.EPollSelectorImpl.doSelect(Unknown Source), sun.nio.ch.SelectorImpl.lockAndDoSelect(Unknown Source), sun.nio.ch.SelectorImpl.select(Unknown Source), io.netty.channel.nio.NioEventLoop.select(NioEventLoop.java:618), io.netty.channel.nio.NioEventLoop.run(NioEventLoop.java:306), io.netty.util.concurrent.SingleThreadEventExecutor$2.run(SingleThreadEventExecutor.java:116), java.lang.Thread.run(Unknown Source)], RUNNABLE pool-11-thread-2 Acceptor0 [email protected]:8123: [sun.nio.ch.ServerSocketChannelImpl.accept0(Native Method), sun.nio.ch.ServerSocketChannelImpl.accept(Unknown Source), org.dynmap.jetty.server.nio.SelectChannelConnector.accept(SelectChannelConnector.java:109), org.dynmap.jetty.server.AbstractConnector$Acceptor.run(AbstractConnector.java:938), java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source), java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source), java.lang.Thread.run(Unknown Source)], RUNNABLE Netty Server IO #2: [sun.nio.ch.EPollArrayWrapper.epollWait(Native Method), sun.nio.ch.EPollArrayWrapper.poll(Unknown Source), sun.nio.ch.EPollSelectorImpl.doSelect(Unknown Source), sun.nio.ch.SelectorImpl.lockAndDoSelect(Unknown Source), sun.nio.ch.SelectorImpl.select(Unknown Source), io.netty.channel.nio.NioEventLoop.select(NioEventLoop.java:618), io.netty.channel.nio.NioEventLoop.run(NioEventLoop.java:306), io.netty.util.concurrent.SingleThreadEventExecutor$2.run(SingleThreadEventExecutor.java:116), java.lang.Thread.run(Unknown Source)], WAITING pool-14-thread-3: [sun.misc.Unsafe.park(Native Method), java.util.concurrent.locks.LockSupport.park(Unknown Source), java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject.await(Unknown Source), java.util.concurrent.LinkedBlockingQueue.take(Unknown Source), java.util.concurrent.ThreadPoolExecutor.getTask(Unknown Source), java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source), java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source), java.lang.Thread.run(Unknown Source)], RUNNABLE Dynmap Render Thread: [java.net.PlainSocketImpl.socketConnect(Native Method), java.net.AbstractPlainSocketImpl.doConnect(Unknown Source), java.net.AbstractPlainSocketImpl.connectToAddress(Unknown Source), java.net.AbstractPlainSocketImpl.connect(Unknown Source), java.net.SocksSocketImpl.connect(Unknown Source), java.net.Socket.connect(Unknown Source), java.net.Socket.connect(Unknown Source), sun.net.NetworkClient.doConnect(Unknown Source), sun.net.www.http.HttpClient.openServer(Unknown Source), sun.net.www.http.HttpClient.openServer(Unknown Source), sun.net.www.http.HttpClient.<init>(Unknown Source), sun.net.www.http.HttpClient.New(Unknown Source), sun.net.www.http.HttpClient.New(Unknown Source), sun.net.www.protocol.http.HttpURLConnection.getNewHttpClient(Unknown Source), sun.net.www.protocol.http.HttpURLConnection.plainConnect(Unknown Source), sun.net.www.protocol.http.HttpURLConnection.connect(Unknown Source), sun.net.www.protocol.http.HttpURLConnection.getInputStream(Unknown Source), java.net.URL.openStream(Unknown Source), javax.imageio.ImageIO.read(Unknown Source), org.dynmap.PlayerFaces$LoadPlayerImages.run(PlayerFaces.java:76), org.dynmap.MapManager$DynmapScheduledThreadPoolExecutor$1.run(MapManager.java:190), org.dynmap.MapManager$DynmapScheduledThreadPoolExecutor$2.run(MapManager.java:206), java.util.concurrent.Executors$RunnableAdapter.call(Unknown Source), java.util.concurrent.FutureTask.run(Unknown Source), java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.access$201(Unknown Source), java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(Unknown Source), java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source), java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source), java.lang.Thread.run(Unknown Source)], RUNNABLE Server thread: [java.lang.Thread.dumpThreads(Native Method), java.lang.Thread.getAllStackTraces(Unknown Source), org.bukkit.craftbukkit.v1_8_R1.CraftCrashReport.call(CraftCrashReport.java:29), net.minecraft.server.v1_8_R1.CrashReportSystemDetails.a(SourceFile:78), net.minecraft.server.v1_8_R1.CrashReport.h(CrashReport.java:43), net.minecraft.server.v1_8_R1.CrashReport.<init>(CrashReport.java:32), net.minecraft.server.v1_8_R1.MinecraftServer.run(MinecraftServer.java:557), java.lang.Thread.run(Unknown Source)], RUNNABLE Query Listener #1: [java.net.PlainDatagramSocketImpl.receive0(Native Method), java.net.AbstractPlainDatagramSocketImpl.receive(Unknown Source), java.net.DatagramSocket.receive(Unknown Source), net.minecraft.server.v1_8_R1.RemoteStatusListener.run(SourceFile:261), java.lang.Thread.run(Unknown Source)], RUNNABLE Netty Server IO #0: [sun.nio.ch.EPollArrayWrapper.epollWait(Native Method), sun.nio.ch.EPollArrayWrapper.poll(Unknown Source), sun.nio.ch.EPollSelectorImpl.doSelect(Unknown Source), sun.nio.ch.SelectorImpl.lockAndDoSelect(Unknown Source), sun.nio.ch.SelectorImpl.select(Unknown Source), io.netty.channel.nio.NioEventLoop.select(NioEventLoop.java:618), io.netty.channel.nio.NioEventLoop.run(NioEventLoop.java:306), io.netty.util.concurrent.SingleThreadEventExecutor$2.run(SingleThreadEventExecutor.java:116), java.lang.Thread.run(Unknown Source)], TIMED_WAITING Craft Scheduler Thread - 7: [sun.misc.Unsafe.park(Native Method), java.util.concurrent.locks.LockSupport.parkNanos(Unknown Source), java.util.concurrent.SynchronousQueue$TransferStack.awaitFulfill(Unknown Source), java.util.concurrent.SynchronousQueue$TransferStack.transfer(Unknown Source), java.util.concurrent.SynchronousQueue.poll(Unknown Source), java.util.concurrent.ThreadPoolExecutor.getTask(Unknown Source), java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source), java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source), java.lang.Thread.run(Unknown Source)], RUNNABLE Thread-9: [java.net.SocketInputStream.socketRead0(Native Method), java.net.SocketInputStream.read(Unknown Source), java.net.SocketInputStream.read(Unknown Source), sun.security.ssl.InputRecord.readFully(Unknown Source), sun.security.ssl.InputRecord.read(Unknown Source), sun.security.ssl.SSLSocketImpl.readRecord(Unknown Source), sun.security.ssl.SSLSocketImpl.readDataRecord(Unknown Source), sun.security.ssl.AppInputStream.read(Unknown Source), java.io.BufferedInputStream.fill(Unknown Source), java.io.BufferedInputStream.read1(Unknown Source), java.io.BufferedInputStream.read(Unknown Source), sun.net.www.http.HttpClient.parseHTTPHeader(Unknown Source), sun.net.www.http.HttpClient.parseHTTP(Unknown Source), sun.net.www.protocol.http.HttpURLConnection.getInputStream(Unknown Source), sun.net.www.protocol.https.HttpsURLConnectionImpl.getInputStream(Unknown Source), ru.tehkode.libs.net.gravitydevelopment.updater.Updater.read(Updater.java:643), ru.tehkode.libs.net.gravitydevelopment.updater.Updater.runUpdater(Updater.java:718), ru.tehkode.libs.net.gravitydevelopment.updater.Updater.access$100(Updater.java:36), ru.tehkode.libs.net.gravitydevelopment.updater.Updater$UpdateRunnable.run(Updater.java:713), java.lang.Thread.run(Unknown Source)], TIMED_WAITING Craft Scheduler Thread - 4: [sun.misc.Unsafe.park(Native Method), java.util.concurrent.locks.LockSupport.parkNanos(Unknown Source), java.util.concurrent.SynchronousQueue$TransferStack.awaitFulfill(Unknown Source), java.util.concurrent.SynchronousQueue$TransferStack.transfer(Unknown Source), java.util.concurrent.SynchronousQueue.poll(Unknown Source), java.util.concurrent.ThreadPoolExecutor.getTask(Unknown Source), java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source), java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source), java.lang.Thread.run(Unknown Source)], WAITING pool-12-thread-1: [sun.misc.Unsafe.park(Native Method), java.util.concurrent.locks.LockSupport.park(Unknown Source), java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject.await(Unknown Source), java.util.concurrent.LinkedBlockingQueue.take(Unknown Source), java.util.concurrent.ThreadPoolExecutor.getTask(Unknown Source), java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source), java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source), java.lang.Thread.run(Unknown Source)], WAITING Finalizer: [java.lang.Object.wait(Native Method), java.lang.ref.ReferenceQueue.remove(Unknown Source), java.lang.ref.ReferenceQueue.remove(Unknown Source), java.lang.ref.Finalizer$FinalizerThread.run(Unknown Source)], RUNNABLE Netty Server IO #3: [sun.nio.ch.EPollArrayWrapper.epollWait(Native Method), sun.nio.ch.EPollArrayWrapper.poll(Unknown Source), sun.nio.ch.EPollSelectorImpl.doSelect(Unknown Source), sun.nio.ch.SelectorImpl.lockAndDoSelect(Unknown Source), sun.nio.ch.SelectorImpl.select(Unknown Source), io.netty.channel.nio.NioEventLoop.select(NioEventLoop.java:618), io.netty.channel.nio.NioEventLoop.run(NioEventLoop.java:306), io.netty.util.concurrent.SingleThreadEventExecutor$2.run(SingleThreadEventExecutor.java:116), java.lang.Thread.run(Unknown Source)], RUNNABLE Dynmap Render Thread: [org.dynmap.hdmap.IsoHDPerspective$OurPerspectiveState.updateSemitransparentLight(IsoHDPerspective.java:167), org.dynmap.hdmap.IsoHDPerspective$OurPerspectiveState.updateLightLevel(IsoHDPerspective.java:207), org.dynmap.hdmap.IsoHDPerspective$OurPerspectiveState.getLightLevelsAtStep(IsoHDPerspective.java:233), org.dynmap.hdmap.ShadowHDLighting.applySmoothLighting(ShadowHDLighting.java:112), org.dynmap.hdmap.ShadowHDLighting.applyLighting(ShadowHDLighting.java:221), org.dynmap.hdmap.TexturePackHDShader$ShaderState.processBlock(TexturePackHDShader.java:222), org.dynmap.hdmap.IsoHDPerspective$OurPerspectiveState.visit_block(IsoHDPerspective.java:554), org.dynmap.hdmap.IsoHDPerspective$OurPerspectiveState.raytrace(IsoHDPerspective.java:648), org.dynmap.hdmap.IsoHDPerspective$OurPerspectiveState.access$300(IsoHDPerspective.java:84), org.dynmap.hdmap.IsoHDPerspective.render(IsoHDPerspective.java:1155), org.dynmap.hdmap.HDMapTile.render(HDMapTile.java:79), org.dynmap.MapManager$FullWorldRenderState.processTile(MapManager.java:708), org.dynmap.MapManager$FullWorldRenderState.run(MapManager.java:641), org.dynmap.MapManager$DynmapScheduledThreadPoolExecutor$1.run(MapManager.java:190), org.dynmap.MapManager$DynmapScheduledThreadPoolExecutor$2.run(MapManager.java:206), java.util.concurrent.Executors$RunnableAdapter.call(Unknown Source), java.util.concurrent.FutureTask.run(Unknown Source), java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.access$201(Unknown Source), java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(Unknown Source), java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source), java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source), java.lang.Thread.run(Unknown Source)], TIMED_WAITING Craft Scheduler Thread - 8: [sun.misc.Unsafe.park(Native Method), java.util.concurrent.locks.LockSupport.parkNanos(Unknown Source), java.util.concurrent.SynchronousQueue$TransferStack.awaitFulfill(Unknown Source), java.util.concurrent.SynchronousQueue$TransferStack.transfer(Unknown Source), java.util.concurrent.SynchronousQueue.poll(Unknown Source), java.util.concurrent.ThreadPoolExecutor.getTask(Unknown Source), java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source), java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source), java.lang.Thread.run(Unknown Source)],}
Recent tasks from 331-361{Essentials:com.earth2me.essentials.EssentialsPlayerListener$1@390,}
Profiler Position: N/A (disabled)
Player Count: 2 / 38; [EntityPlayer['BruhtatoChips'/255, l='world', x=-2802.51, y=74.00, z=157.26](BruhtatoChips at -2802.514882474564,74.0,157.25512731807066), EntityPlayer['CreeperChaos'/542, l='world', x=-2808.70, y=70.00, z=272.23](CreeperChaos at -2808.699999988079,70.0,272.2307905731865)]
Is Modded: Definitely; Server brand changed to 'Spigot'
Type: Dedicated Server (map_server.txt)

 

unfortunately I do not know why it crashed. Though I do know the reason data was lost. The server saves all data in the background on its own, with a timer. The crash happened in between saves, causing the server to revert back to the last save.

 

That was my thought too, except that's not how it seems, it didn't revert to the last save, it literally removed all progress from everyone who was online. like their user data was completely deleted. In any case I don't know what caused the first crash, but the first one corrupted a chunk causing the subsequent crashes whenever specific players logged in. I had to run region fixer and now it's working properly as far as I can tell.

Edit: NO.... No it isn't working properly. I keep getting these crashes, and it seems to be only when one player joins my server. And no, I'm not banning him, he's a friend of mine so I need to know how to fix it so that he can join again.

 

try deleting ALL of their player data, the .dat file from the world folder, and if you are using essentials (or something similar) remove that file as well. That will cause the server to think they are a brand new player as one of those files could be corrupted.