2 hours of play getting erased/ regenerated

Running 1.7.2, 1 gig server, normally 400-600 mb free at all times, normally runs at 50%, cpu hardly ever spikes unless reloading of course, 28 plugins, no errors that i know or, but yesterday i started getting this error when ever the last person on the server logs out, it rolls back anything that was built, was playing as a normal player, digging a mine, then when i logged off, this happend:
Using multicraft as console, it scrolls backwards, so the older messages are up top, ones from earlier at bottom... annoying.

22.03 02:05:36 [Multicraft] Skipped 40 lines due to rate limit (30/s)
22.03 02:05:21 [Server] INFO at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) ~[?:1.7.0_09-icedtea]
22.03 02:05:21 [Server] INFO at me.Awezomedude235.SimpleChatLogger.PlayerKillListener.onPlayerChat(PlayerKillListener.java:26) ~[?:?]
22.03 02:05:21 [Server] INFO Caused by: java.lang.NullPointerException
22.03 02:05:21 [Server] INFO at net.minecraft.server.v1_7_R1.ThreadServerApplication.run(SourceFile:617) [craftbukkit-1.7.2.jar:git-Bukkit-1.6.4-R2.0-21-gcf51e92-b2938jnks]
22.03 02:05:21 [Server] INFO at net.minecraft.server.v1_7_R1.MinecraftServer.run(MinecraftServer.java:453) [craftbukkit-1.7.2.jar:git-Bukkit-1.6.4-R2.0-21-gcf51e92-b2938jnks]
22.03 02:05:21 [Server] INFO at net.minecraft.server.v1_7_R1.MinecraftServer.t(MinecraftServer.java:541) [craftbukkit-1.7.2.jar:git-Bukkit-1.6.4-R2.0-21-gcf51e92-b2938jnks]
22.03 02:05:21 [Server] INFO at net.minecraft.server.v1_7_R1.DedicatedServer.u(DedicatedServer.java:250) [craftbukkit-1.7.2.jar:git-Bukkit-1.6.4-R2.0-21-gcf51e92-b2938jnks]
22.03 02:05:21 [Server] INFO at net.minecraft.server.v1_7_R1.MinecraftServer.u(MinecraftServer.java:651) [craftbukkit-1.7.2.jar:git-Bukkit-1.6.4-R2.0-21-gcf51e92-b2938jnks]
22.03 02:05:21 [Server] INFO at net.minecraft.server.v1_7_R1.ServerConnection.c(SourceFile:134) [craftbukkit-1.7.2.jar:git-Bukkit-1.6.4-R2.0-21-gcf51e92-b2938jnks]
22.03 02:05:21 [Server] INFO at net.minecraft.server.v1_7_R1.NetworkManager.a(NetworkManager.java:146) [craftbukkit-1.7.2.jar:git-Bukkit-1.6.4-R2.0-21-gcf51e92-b2938jnks]
22.03 02:05:21 [Server] INFO at net.minecraft.server.v1_7_R1.PacketPlayInPosition.handle(SourceFile:63) [craftbukkit-1.7.2.jar:git-Bukkit-1.6.4-R2.0-21-gcf51e92-b2938jnks]
22.03 02:05:21 [Server] INFO at net.minecraft.server.v1_7_R1.PacketPlayInFlying.a(SourceFile:137) [craftbukkit-1.7.2.jar:git-Bukkit-1.6.4-R2.0-21-gcf51e92-b2938jnks]
22.03 02:05:21 [Server] INFO at net.minecraft.server.v1_7_R1.PlayerConnection.a(PlayerConnection.java:339) [craftbukkit-1.7.2.jar:git-Bukkit-1.6.4-R2.0-21-gcf51e92-b2938jnks]
22.03 02:05:21 [Server] INFO at net.minecraft.server.v1_7_R1.EntityPlayer.i(EntityPlayer.java:240) [craftbukkit-1.7.2.jar:git-Bukkit-1.6.4-R2.0-21-gcf51e92-b2938jnks]
22.03 02:05:21 [Server] INFO at net.minecraft.server.v1_7_R1.EntityHuman.h(EntityHuman.java:162) [craftbukkit-1.7.2.jar:git-Bukkit-1.6.4-R2.0-21-gcf51e92-b2938jnks]
22.03 02:05:21 [Server] INFO at net.minecraft.server.v1_7_R1.EntityLiving.h(EntityLiving.java:1258) [craftbukkit-1.7.2.jar:git-Bukkit-1.6.4-R2.0-21-gcf51e92-b2938jnks]
22.03 02:05:21 [Server] INFO at net.minecraft.server.v1_7_R1.Entity.h(Entity.java:238) [craftbukkit-1.7.2.jar:git-Bukkit-1.6.4-R2.0-21-gcf51e92-b2938jnks]
22.03 02:05:21 [Server] INFO at net.minecraft.server.v1_7_R1.EntityLiving.C(EntityLiving.java:148) [craftbukkit-1.7.2.jar:git-Bukkit-1.6.4-R2.0-21-gcf51e92-b2938jnks]
22.03 02:05:21 [Server] INFO at net.minecraft.server.v1_7_R1.EntityPlayer.damageEntity(EntityPlayer.java:446) [craftbukkit-1.7.2.jar:git-Bukkit-1.6.4-R2.0-21-gcf51e92-b2938jnks]
22.03 02:05:21 [Server] INFO at net.minecraft.server.v1_7_R1.EntityHuman.damageEntity(EntityHuman.java:746) [craftbukkit-1.7.2.jar:git-Bukkit-1.6.4-R2.0-21-gcf51e92-b2938jnks]
22.03 02:05:21 [Server] INFO at net.minecraft.server.v1_7_R1.EntityLiving.damageEntity(EntityLiving.java:725) [craftbukkit-1.7.2.jar:git-Bukkit-1.6.4-R2.0-21-gcf51e92-b2938jnks]
22.03 02:05:21 [Server] INFO at net.minecraft.server.v1_7_R1.EntityPlayer.die(EntityPlayer.java:368) [craftbukkit-1.7.2.jar:git-Bukkit-1.6.4-R2.0-21-gcf51e92-b2938jnks]
22.03 02:05:21 [Server] INFO at org.bukkit.craftbukkit.v1_7_R1.event.CraftEventFactory.callPlayerDeathEvent(CraftEventFactory.java:345) [craftbukkit-1.7.2.jar:git-Bukkit-1.6.4-R2.0-21-gcf51e92-b2938jnks]
22.03 02:05:21 [Server] INFO at org.bukkit.plugin.SimplePluginManager.callEvent(SimplePluginManager.java:462) [craftbukkit-1.7.2.jar:git-Bukkit-1.6.4-R2.0-21-gcf51e92-b2938jnks]
22.03 02:05:21 [Server] INFO at org.bukkit.plugin.SimplePluginManager.fireEvent(SimplePluginManager.java:477) [craftbukkit-1.7.2.jar:git-Bukkit-1.6.4-R2.0-21-gcf51e92-b2938jnks]
22.03 02:05:21 [Server] INFO at org.bukkit.plugin.RegisteredListener.callEvent(RegisteredListener.java:62) ~[craftbukkit-1.7.2.jar:git-Bukkit-1.6.4-R2.0-21-gcf51e92-b2938jnks]
22.03 02:05:21 [Server] INFO at org.bukkit.plugin.java.JavaPluginLoader$1.execute(JavaPluginLoader.java:427) ~[craftbukkit-1.7.2.jar:git-Bukkit-1.6.4-R2.0-21-gcf51e92-b2938jnks]
22.03 02:05:21 [Server] INFO org.bukkit.event.EventException
22.03 02:05:21 [Server] ERROR Could not pass event PlayerDeathEvent to SimpleChatLogger v1.06
22.03 02:05:15 [Server] INFO LostExplorer: [NotDaMomma]NinjarakuPwnz
22.03 02:05:09 [Multicraft] NinjarakuPwnz ran command Message of the Day
22.03 02:05:09 [Connect] User NinjarakuPwnz, IP hidden =p
22.03 02:05:09 [Server] INFO UUID of player NinjarakuPwnz is hidden =p
22.03 02:05:05 [Server] INFO NinjarakuPwnz left the game.
22.03 02:05:05 [Disconnect] User NinjarakuPwnz has disconnected, reason: Disconnected
22.03 02:04:56 [Multicraft] NinjarakuPwnz ran command Message of the Day
22.03 02:04:56 [Connect] User NinjarakuPwnz, IP hidden =p
22.03 02:04:56 [Server] INFO UUID of player NinjarakuPwnz is hidden =p
22.03 02:00:00 [Multicraft] Server ran command Admin Say
22.03 01:59:46 [Server] INFO NinjarakuPwnz left the game.
22.03 01:59:46 [Disconnect] User NinjarakuPwnz has disconnected, reason: Disconnected
22.03 01:59:30 [Server] INFO LostExplorer: [NotDaMomma]NinjarakuPwnz
22.03 01:58:52 [Server] INFO LostExplorer: [NotDaMomma]NinjarakuPwnz
22.03 01:58:13 [Server] INFO LostExplorer: [NotDaMomma]NinjarakuPwnz
22.03 01:57:35 [Server] INFO LostExplorer: [NotDaMomma]NinjarakuPwnz
22.03 01:56:57 [Server] INFO LostExplorer: [NotDaMomma]NinjarakuPwnz
22.03 01:56:18 [Server] INFO LostExplorer: [NotDaMomma]NinjarakuPwnz
22.03 01:55:40 [Server] INFO LostExplorer: [NotDaMomma]NinjarakuPwnz
22.03 01:55:02 [Server] INFO LostExplorer: [NotDaMomma]NinjarakuPwnz
22.03 01:54:23 [Server] INFO LostExplorer: [NotDaMomma]NinjarakuPwnz
22.03 01:53:45 [Server] INFO LostExplorer: [NotDaMomma]NinjarakuPwnz
22.03 01:53:07 [Server] INFO LostExplorer: [NotDaMomma]NinjarakuPwnz
22.03 01:52:28 [Server] INFO LostExplorer: [NotDaMomma]NinjarakuPwnz
22.03 01:51:50 [Server] INFO LostExplorer: [NotDaMomma]NinjarakuPwnz
22.03 01:51:24 [Server] INFO §a§4[NotDaMomma]§fNinjarakuPwnz§r §asold cobblestone for §a$12.90 §a(129 items at $0.10 each).
22.03 01:51:12 [Server] INFO LostExplorer: [NotDaMomma]NinjarakuPwnz
22.03 01:50:33 [Server] INFO LostExplorer: [NotDaMomma]NinjarakuPwnz
22.03 01:49:55 [Server] INFO LostExplorer: [NotDaMomma]NinjarakuPwnz
22.03 01:49:17 [Server] INFO LostExplorer: [NotDaMomma]NinjarakuPwnz
22.03 01:48:38 [Server] INFO LostExplorer: [NotDaMomma]NinjarakuPwnz
22.03 01:48:00 [Server] INFO LostExplorer: [NotDaMomma]NinjarakuPwnz
22.03 01:47:22 [Server] INFO LostExplorer: [NotDaMomma]NinjarakuPwnz
22.03 01:46:49 [Server] WARN Can't keep up! Did the system time change, or is the server overloaded? Running 2462ms behind, skipping 49 tick(s)
22.03 01:46:43 [Server] INFO LostExplorer: [NotDaMomma]NinjarakuPwnz
22.03 01:46:38 [Server] INFO §a§4[NotDaMomma]§fNinjarakuPwnz§r §asold cobblestone for §a$2.40 §a(24 items at $0.10 each).
22.03 01:46:17 [Server] INFO World saved.
22.03 01:46:17 [Server] INFO CONSOLE: Forcing save..
22.03 01:46:17 [Server] INFO CONSOLE: Enabled level saving..
22.03 01:46:17 [Multicraft] Auto-saving world...
22.03 01:46:05 [Server] INFO LostExplorer: [NotDaMomma]NinjarakuPwnz
22.03 01:45:27 [Server] INFO LostExplorer: [NotDaMomma]NinjarakuPwnz
22.03 01:45:00 [Multicraft] Server ran command Admin Say
22.03 01:44:48 [Server] INFO LostExplorer: [NotDaMomma]NinjarakuPwnz
22.03 01:44:10 [Server] INFO LostExplorer: [NotDaMomma]NinjarakuPwnz
22.03 01:43:32 [Server] INFO LostExplorer: [NotDaMomma]NinjarakuPwnz
22.03 01:42:53 [Server] INFO LostExplorer: [NotDaMomma]NinjarakuPwnz
22.03 01:42:15 [Server] INFO LostExplorer: [NotDaMomma]NinjarakuPwnz
22.03 01:41:36 [Server] INFO LostExplorer: [NotDaMomma]NinjarakuPwnz
22.03 01:41:36 [Server] WARN Can't keep up! Did the system time change, or is the server overloaded? Running 2317ms behind, skipping 46 tick(s)

Anything earlier then this was just console giving the 10 min MOTD and listing which players were on, no error or can't keep up messages. When i logged back on a minute later, everything i was doing for the past 2 hours was rolled back to how the hill side was before i did anything to it, 2 whole hours just rolled back, never had this issue before. But I Did add BattleArena and the spleef, ctf plugins to go with it, and since then this has been happening. i tried to edit the same area, log out, no one on the server, but can't re-create the problem, except its happening 2 nights in a row now.

Have 3 worlds, main world for survival, factions, towns, spawn, another for arenas and minigames, and another for resources, this is occurring in the same area 2 nights in a row in my main world, which was the original world from the start of the server.

I set all plugins to "auto-update: false" could this be the problem? or does it matter?

I logged out for a few minutes after deleting all the scheduled console commands on multicraft, i did since the last post again was rolled back within 10 minutes, what in the heck could be doing this? im building within my WorldBorder area, the stuff other players made earlier is still there so its either not rolling back vary far, or just rolling back what I build. doing mroe tests to see if its what is done close to world border's border, if its happening in all worlds, will keep updated =p

its not letting me edit my posts even though theres a button for it, was going to add that i get this:

22.03 02:46:42 [Server] INFO
Followed by about 20 blank lines in console...

Issue is with WorldBorder, It's re-filling WITHIN about 200 blocks of the world each time the world saves and players are no in the active chunk, i tried with bypass on, build a line of blocks from within the border, to well beyond it, disabled bypass, could not go outside the border as expected, Logged out for a few minutes, logged back in, and boom, problem re created.

Worldborder's config:

cfg-version: 9
message: '&cYou have reached this world's set border.'
round-border: true
debug-mode: false
whoosh-effect: false
portal-redirection: true
knock-back-dist: 3.0
timer-delay-ticks: 5
remount-delay-ticks: 0
dynmap-border-enabled: true
dynmap-border-message: The border of the world.
player-killed-bad-spawn: false
deny-enderpearl: false
fill-autosave-frequency: 30
bypass-list:
- ninjarakupwnz
worlds:
Player_Towns:
x: 177.5473133972614
z: 218.2049623208834
radiusX: 1000
radiusZ: 1000
wrapping: false
BattleFront:
x: 49.43134057674308
z: 260.49737365739605
radiusX: 500
radiusZ: 500
wrapping: false
resource:
x: -17.514458191408576
z: 181.56071073044185
radiusX: 500
radiusZ: 500
wrapping: false

EDIT by Moderator: merged posts, please use the edit button instead of double posting.

 

found issue
Worldborder was resetting the chunks that were close to the worlds set border since it was set to "round" it was cofusing its own border where to not fill/blend when the chunk becomes inactive, didn't need to log out, it even does this when there are no players in the area. I deleted ALL worldborder files with server off, re-installed worldborder, setup new border as "Square" problem solved.

JUST WANTED TO THANK EVERYONE FOR YOUR HELP!... not even a single "hey try this" =) your welcome, if anyone else runs into this issue

 

Kind of getting a sarcasm vibe from this... Some of us that like to help just didn't have any suggestions or ideas. I saw your post and had no idea what could be causing your problems since I've never encountered it and never used WorldBorder. It's reasonable to suppose that most of your other views were also people who didn't know what to suggest.
Thanks though for adding the solution you found to the post; I'm sure it will help someone else in the future.