World Destroying Itself

I've been running a craftbukkit server for almost a year now, but ever since 1.2.3 came out it's been acting up. I'm having the most peculiar problem: Whenever I restart my server or upload a new world the server appears to generate a new map on top of it. This used to be a massive island, but an ocean appears to have cut it in half and in squares. It happens when I let the server generate a map, chunk holes appear, giant strips of land is home to all new terrain, and it's extremely annoying.

I rent from Xenon Servers. They're customer support, which is usually very knowledgeable and overall stellar, said it looked to be a problem with Worldedit. I reinstalled craftbukkit and didn't install Worldedit, yet it still continued to do it. With no unusual errors, they told me they were stumped and couldn't help any further. Now I've tried it on my home computer with no pluggins and it works just fine. Since then, I've been experimenting with different combinations, removing pluggins that might be causing it, but it's extremely tedious as Xenon uses TC Admin. I don't have time to continue to experiment, and the server's two month downtime has sent the community after greener pastures. I'm at a loss, anyone have any ideas?

I'm using:
Factions
War!
Ancient Gates
Multiverse Core
Saga
Needtown
EagleEye
Essentials, Essentials Chat, Essentials Group Manager
iConomy
Chestshop
and Starter Kit

My server log:

Code:

2012-11-21 09:25:55 [INFO] Starting minecraft server version 1.4.5
2012-11-21 09:25:55 [INFO] Loading properties
2012-11-21 09:25:55 [INFO] Default game type: SURVIVAL
2012-11-21 09:25:55 [INFO] Generating keypair
2012-11-21 09:25:55 [INFO] Starting Minecraft server on 50.31.23.136:25565
2012-11-21 09:25:56 [INFO] This server is running CraftBukkit version git-Bukkit-1.4.5-R0.1-b2483jnks (MC: 1.4.5) (Implementing API version 1.4.5-R0.1)
2012-11-21 09:25:57 [SEVERE] ----- Bukkit Auto Updater -----
2012-11-21 09:25:57 [SEVERE] Your version of CraftBukkit is known to be broken. It is strongly advised that you update to a more recent version ASAP.
2012-11-21 09:25:57 [SEVERE] Known issues with your version:
2012-11-21 09:25:57 [SEVERE] > This build allows players to infinitely spawn baby animals, plugins to leave players in an untouchable state, among other things. Upgrading to the latest beta is highly recommended.
2012-11-21 09:25:57 [SEVERE] Unfortunately, there is not yet a newer version suitable for your server. We would advise you wait an hour or two, or try out a dev build.
2012-11-21 09:25:57 [SEVERE] ----- ------------------- -----
2012-11-21 09:25:57 [INFO] [AncientGates] Loading AncientGates v1.4.1
2012-11-21 09:25:57 [INFO] [EagleEye] Loading EagleEye v1.1.3
2012-11-21 09:25:57 [INFO] [DFarm] Loading DFarm v0.8.2
2012-11-21 09:25:57 [INFO] [GroupManager] Loading GroupManager v2.0.61 (Phoenix)
2012-11-21 09:25:57 [INFO] [iConomy] Loading iConomy v7.0
2012-11-21 09:25:57 [INFO] [NeedTown] Loading NeedTown v2.3.7
2012-11-21 09:25:57 [INFO] [StarterKit] Loading StarterKit v1.2.6
2012-11-21 09:25:57 [INFO] [War] Loading War v1.7.2 (Doolittle)
2012-11-21 09:25:57 [INFO] [Multiverse-Core] Loading Multiverse-Core v2.4-b527
2012-11-21 09:25:57 [INFO] [FreedomMessage] Loading FreedomMessage v1.0
2012-11-21 09:25:57 [INFO] [Essentials] Loading Essentials v2.9.4
2012-11-21 09:25:57 [INFO] [Saga] Loading Saga v0.5
2012-11-21 09:25:57 [INFO] [ChestShop] Loading ChestShop v3.46
2012-11-21 09:25:57 [INFO] [EssentialsChat] Loading EssentialsChat v2.9.4
2012-11-21 09:25:57 [INFO] [Factions] Loading Factions v1.6.9.2
2012-11-21 09:25:57 [INFO] Preparing level "world"
2012-11-21 09:25:57 [INFO] Preparing start region for level 0 (Seed: 202961)
2012-11-21 09:25:58 [INFO] Preparing spawn area: 4%
2012-11-21 09:25:59 [INFO] Preparing spawn area: 20%
2012-11-21 09:26:00 [INFO] Preparing spawn area: 36%
2012-11-21 09:26:01 [INFO] Preparing spawn area: 48%
2012-11-21 09:26:02 [INFO] Preparing spawn area: 57%
2012-11-21 09:26:03 [INFO] Preparing spawn area: 69%
2012-11-21 09:26:04 [INFO] Preparing spawn area: 81%
2012-11-21 09:26:05 [INFO] Preparing spawn area: 93%
2012-11-21 09:26:06 [INFO] Preparing start region for level 1 (Seed: 3278297219550133153)
2012-11-21 09:26:06 [INFO] Preparing spawn area: 0%
2012-11-21 09:26:07 [INFO] Preparing spawn area: 12%
2012-11-21 09:26:09 [INFO] Preparing spawn area: 24%
2012-11-21 09:26:10 [INFO] Preparing spawn area: 36%
2012-11-21 09:26:11 [INFO] Preparing spawn area: 48%
2012-11-21 09:26:12 [INFO] Preparing spawn area: 61%
2012-11-21 09:26:13 [INFO] Preparing spawn area: 69%
2012-11-21 09:26:14 [INFO] Preparing spawn area: 81%
2012-11-21 09:26:15 [INFO] Preparing spawn area: 93%
2012-11-21 09:26:15 [INFO] Preparing start region for level 2 (Seed: 3278297219550133153)
2012-11-21 09:26:16 [INFO] Preparing spawn area: 8%
2012-11-21 09:26:17 [INFO] Preparing spawn area: 36%
2012-11-21 09:26:18 [INFO] Preparing spawn area: 57%
2012-11-21 09:26:19 [INFO] Preparing spawn area: 81%
2012-11-21 09:26:19 [INFO] [AncientGates] Enabling AncientGates v1.4.1
2012-11-21 09:26:19 [INFO] [AncientGates v1.4.1] Loading conf from disk
2012-11-21 09:26:19 [INFO] [AncientGates v1.4.1] Loading gates from disk
2012-11-21 09:26:19 [INFO] [AncientGates v1.4.1] Enabled
2012-11-21 09:26:19 [INFO] [EagleEye] Enabling EagleEye v1.1.3
2012-11-21 09:26:20 [INFO] [EagleEye] ------[EagleEye Updates Checker]------
2012-11-21 09:26:20 [INFO] [EagleEye] EagleEye is up to date.
2012-11-21 09:26:20 [INFO] [EagleEye] --------------------------------------
2012-11-21 09:26:20 [INFO] [EagleEye] Loading events...
2012-11-21 09:26:20 [INFO] [EagleEye] Loading commands...
2012-11-21 09:26:20 [INFO] [EagleEye] EagleEye 1.1.3 (made by ElectronGuigui) enabled
2012-11-21 09:26:20 [INFO] [DFarm] Enabling DFarm v0.8.2
2012-11-21 09:26:20 [INFO] [DFarm] [AutoUpdate] v1.3 enabled!
2012-11-21 09:26:20 [SEVERE] Error occurred while enabling DFarm v0.8.2 (Is it up to date?)
java.lang.NumberFormatException: multiple points
    at sun.misc.FloatingDecimal.readJavaFormatString(Unknown Source)
    at java.lang.Double.parseDouble(Unknown Source)
    at me.Vandrake.farm.farm.onEnable(farm.java:33)
    at org.bukkit.plugin.java.JavaPlugin.setEnabled(JavaPlugin.java:217)
    at org.bukkit.plugin.java.JavaPluginLoader.enablePlugin(JavaPluginLoader.java:374)
    at org.bukkit.plugin.SimplePluginManager.enablePlugin(SimplePluginManager.java:381)
    at org.bukkit.craftbukkit.CraftServer.loadPlugin(CraftServer.java:270)
    at org.bukkit.craftbukkit.CraftServer.enablePlugins(CraftServer.java:252)
    at net.minecraft.server.MinecraftServer.j(MinecraftServer.java:320)
    at net.minecraft.server.MinecraftServer.e(MinecraftServer.java:299)
    at net.minecraft.server.MinecraftServer.a(MinecraftServer.java:258)
    at net.minecraft.server.DedicatedServer.init(DedicatedServer.java:147)
    at net.minecraft.server.MinecraftServer.run(MinecraftServer.java:398)
    at net.minecraft.server.ThreadServerApplication.run(SourceFile:856)
2012-11-21 09:26:20 [INFO] [GroupManager] Enabling GroupManager v2.0.61 (Phoenix)
2012-11-21 09:26:20 [INFO] GroupManager version 2.0.61 (Phoenix) is enabled!
2012-11-21 09:26:20 [INFO] [iConomy] Enabling iConomy v7.0
2012-11-21 09:26:20 [INFO] [iConomy - April Fools] Enabled (41 ms)
2012-11-21 09:26:20 [INFO] [iConomy] Hello, I'm Nijikokun. Yes, this is an April Fools joke, but '/money top' was fixed! Enjoy :) - Rare Version!
2012-11-21 09:26:20 [INFO] [iConomy - April Fools] Purged accounts with default balance.
2012-11-21 09:26:20 [INFO] [NeedTown] Enabling NeedTown v2.3.7
2012-11-21 09:26:20 [INFO] [NeedTown] Enabled Version 2.3.7 by jacklin213
2012-11-21 09:26:20 [INFO] [StarterKit] Enabling StarterKit v1.2.6
2012-11-21 09:26:20 [INFO] [War] Enabling War v1.7.2 (Doolittle)
2012-11-21 09:26:20 [INFO] [War] War v1.7.2 (Doolittle) is on.
2012-11-21 09:26:20 [INFO] [Multiverse-Core] Enabling Multiverse-Core v2.4-b527
2012-11-21 09:26:20 [INFO] [Multiverse-Core] - Version 2.4-b527 (API v14) Enabled - By Rigby, fernferret, lithium3141 and main--
2012-11-21 09:26:20 [INFO] [AllPay] - Version 10.0 - hooked into iConomy 6 for Multiverse-Core v2.4-b527
2012-11-21 09:26:21 [INFO] [Multiverse-Core] Loading World & Settings - 'world' - Env: NORMAL - Type: NORMAL & seed: 202961
2012-11-21 09:26:21 [INFO] [Multiverse-Core] Loading World & Settings - 'world_nether' - Env: NETHER - Type: NORMAL & seed: 263804186401875161
2012-11-21 09:26:21 [WARNING] [Multiverse-Core] Spawn location from world.dat file was unsafe. Adjusting...
2012-11-21 09:26:21 [WARNING] [Multiverse-Core] Original Location: X: 0 Y: 64 Z: 0 P: 0 Y: 0
2012-11-21 09:26:21 [INFO] [Multiverse-Core] New Spawn for 'world_nether' is Located at: world_nether:-0.50,64.00,-0.50:0.00:0.00
2012-11-21 09:26:21 [INFO] [Multiverse-Core] Loading World & Settings - 'world_the_end' - Env: THE_END - Type: NORMAL & seed: 263804186401875161
2012-11-21 09:26:21 [WARNING] [Multiverse-Core] Spawn location from world.dat file was unsafe. Adjusting...
2012-11-21 09:26:21 [WARNING] [Multiverse-Core] Original Location: X: 0 Y: 50 Z: 0 P: 0 Y: 0
2012-11-21 09:26:21 [INFO] [Multiverse-Core] New Spawn for 'world_the_end' is Located at: world_the_end:0.00,63.00,0.00:0.00:0.00
2012-11-21 09:26:21 [INFO] [Multiverse-Core] 3 - World(s) loaded.
2012-11-21 09:26:21 [INFO] [FreedomMessage] Enabling FreedomMessage v1.0
2012-11-21 09:26:21 [INFO] [FreedomMessage] FreedomMessage Enable!
2012-11-21 09:26:21 [INFO] [Essentials] Enabling Essentials v2.9.4
2012-11-21 09:26:22 [INFO] Essentials: Using GroupManager based permissions.
2012-11-21 09:26:22 [INFO] [Essentials] Payment method found (iConomy version: 6)
2012-11-21 09:26:22 [INFO] [Saga] Enabling Saga v0.5
2012-11-21 09:26:22 [INFO] Enabling Saga.
2012-11-21 09:26:22 [INFO] Using GroupManager permissions.
2012-11-21 09:26:22 [INFO] Using default economy.
2012-11-21 09:26:22 [INFO] Using GroupManager chat.
2012-11-21 09:26:22 [INFO] Loading statistics.
2012-11-21 09:26:22 [INFO] Loading bundles.
2012-11-21 09:26:22 [INFO] Loading factions.
2012-11-21 09:26:22 [INFO] Loading faction claims.
2012-11-21 09:26:22 [INFO] Saga enabled.
2012-11-21 09:26:22 [INFO] [ChestShop] Enabling ChestShop v3.46
2012-11-21 09:26:22 [INFO] [ChestShop] Essentials version 2.8.2 loaded.
2012-11-21 09:26:22 [INFO] [EssentialsChat] Enabling EssentialsChat v2.9.4
2012-11-21 09:26:22 [INFO] [Factions] Enabling Factions v1.6.9.2
2012-11-21 09:26:22 [INFO] [Factions v1.6.9.2] === ENABLE START ===
2012-11-21 09:26:22 [INFO] [Factions v1.6.9.2] Loading board from disk
2012-11-21 09:26:22 [INFO] [Factions v1.6.9.2] Found and will integrate chat with EssentialsChat v2.9.4
2012-11-21 09:26:22 [INFO] [Factions v1.6.9.2] Economy integration is disabled, and the plugin "Vault" is not installed.
2012-11-21 09:26:23 [INFO] [Factions v1.6.9.2] === ENABLE DONE (Took 222ms) ===
2012-11-21 09:26:23 [INFO] Server permissions file permissions.yml is empty, ignoring it
2012-11-21 09:26:23 [INFO] Done (25.846s)! For help, type "help" or "?"
2012-11-21 09:26:24 [INFO] /68.45.174.66:52856 lost connection
2012-11-21 09:26:42 [INFO] Staffenburg[/68.45.174.66:52898] logged in with entity id 5488 at ([world] 29.375313111224905, 100.97483775184138, 47.14697173864292)
2012-11-21 09:26:42 [INFO] Loading Saga player for Staffenburg.
2012-11-21 09:27:58 [INFO] Connection reset
2012-11-21 09:27:58 [INFO] Staffenburg lost connection: disconnect.quitting
2012-11-21 09:27:58 [INFO] Unloading saga player for Staffenburg.

 

It maybe that you have a corrupted world. Also, you might want to get rid of the plugin "DFarm v0.8.2"

 

I thought that at first too, but it happens with multiple worlds. Every world I either generate or put in there does this.

 

It looks like its using different seeds. Are the seed values for each world consistent every time the server starts?