Okay, so this has been happening for quite a bit. At first, I thought it might have been related to some plugins I recently installed although after disabling them, it still happens. I updated Bukkit from 1.4.6 (which was also happening) to 1.4.7 today and it's still occurring. Code: java.lang.ArrayIndexOutOfBoundsException: -13 at net.minecraft.server.v1_4_R1.ChunkSection.a(ChunkSection.java:41) at net.minecraft.server.v1_4_R1.Chunk.getTypeId(Chunk.java:350) at net.minecraft.server.v1_4_R1.Chunk.a(Chunk.java:640) at net.minecraft.server.v1_4_R1.Chunk.a(Chunk.java:627) at net.minecraft.server.v1_4_R1.ChunkRegionLoader.loadEntities(ChunkRegionLoader.java:350) at org.bukkit.craftbukkit.v1_4_R1.chunkio.ChunkIOProvider.callStage2(ChunkIOProvider.java:47) at org.bukkit.craftbukkit.v1_4_R1.chunkio.ChunkIOProvider.callStage2(ChunkIOProvider.java:13) at org.bukkit.craftbukkit.v1_4_R1.util.AsynchronousExecutor$Task.finish(AsynchronousExecutor.java:179) at org.bukkit.craftbukkit.v1_4_R1.util.AsynchronousExecutor.finishActive(AsynchronousExecutor.java:287) at org.bukkit.craftbukkit.v1_4_R1.chunkio.ChunkIOExecutor.tick(ChunkIOExecutor.java:30) at net.minecraft.server.v1_4_R1.MinecraftServer.r(MinecraftServer.java:537) at net.minecraft.server.v1_4_R1.DedicatedServer.r(DedicatedServer.java:224) at net.minecraft.server.v1_4_R1.MinecraftServer.q(MinecraftServer.java:494) at net.minecraft.server.v1_4_R1.MinecraftServer.run(MinecraftServer.java:427) at net.minecraft.server.v1_4_R1.ThreadServerApplication.run(SourceFile:849)
Make sure your plugins are updated, i recommend you use the craft bukkit up to date plugin find it at http://dev.bukkit.org/server-mods/craftbukkituptodate/ It doesn't auto update your plugins it downloads new versions in the bukkit_update folder so you will have to manually update them.
I already have a plugin that checks if there are any updates to my plugins and all my plugins are up to date. I don't have any old plugins that are inactive anymore either.
So would I have to use like chunkster to fix it? -edit- Since chunkster is outdated, I tried using Minecraft region fixer which I can't seem to get working. I read somewhere that you can use MCedit to fix it but it won't work either. Any suggestions?