Chunk Errors switching from Vanilla

I'm trying to set up my server as a Bukkit server and I am switching from Vanilla. In our world there is a severe chunk error that causes the server to crash. Rather than making a new world, we all agreed just not to go there, it's far enough away that it wasn't a problem. Now, I believe it is what is interfering with this transition.

I'm getting the following error message:
[SEVERE} Unexpected exception
java.lang.NullPointerException
at net.minecraft.server.WorldServer.c(WorldServer.java:106)
at net.minecraft.server.World.a(World.java:2078)
at net.minecraft.server.Chunk.addEntities(Chunk.java:470)
at net.minecraft.server.ChunkProviderServer.getChunkAt(ChunkProviderServer.java:118)
at net.minecraft.server.ChunkProviderServer.getOrCreateChunk(ChunkProviderServer.java:118)
at net.minecraft.server.World.getChunkAt(World.java:280)
at net.minecraft.server.World.getTypeId(World.java:227)
at net.minecraft.server.World.isEmpty(World.java:231)
at net.minecraft.server.World.a(World.java:198)
at net.minecraft.server.WorldProviderHell.canSpawn(World.java:98)
at net.minecraft.server.World.canSpawn(World.java:98)
at net.minecraft.server.World.c(World.java:148)
at net.minecraft.server.World.<init>(World.java:186)
at net.minecraft.server.WorldServer.<init>(WorldServer.java:148)
at net.minecraft.server.SecondaryWorldServer.<init>(SecondaryWorldServer.java:8)
at net.minecraft.server.MinecraftServer.a(MinecraftServer.java:211)
at net.minecraft.server.MinecraftServer.init(MinecraftServer.java:149)
at net.minecraft.server.MinecraftServer.run(MinecraftServer.java:337)
at net.minecraft.server.ThreadServerApplication.run(SourceFile:422)

I'm also trying to stop the server, and all I'm getting is the "I'm sorry, Dave, but I cannot let you do that." response. Any help would be greatly appreciated.

More Info:
Linux ubuntu 2.6.35-22-server #33-Ubuntu SMP Sun Sep 19 20:48:58 UTC 2010 x86_64 GNU/Linux
java version "1.6.0_22"
Java(TM) SE Runtime Environment (build 1.6.0_22-b04)
Java HotSpot(TM) 64-Bit Server VM (build 17.1-b03, mixed mode)
Running CraftBukkit 1060
No Plugins

More More Info:
Just tried running CraftBukkit without the old world folder, no problem.

More More More Info:
Fired up MCEdit. Deleted the offending chunks. Still not working. Vanilla runs just fine.

 

I'm also having the same problems with craftbukkit, both the null pointer and the dave message. No problems with vanilla, but have tried with a brand spanking clean new map but the problem persists, so its not just a problem with switching to bukkit from vanilla.

Info
Ubuntu 10.04 32bit
Linux link 2.6.32-33-generic #72-Ubuntu SMP Fri Jul 29 21:08:37 UTC 2011 i686 GNU/Linux
java version "1.6.0_26"
Java(TM) SE Runtime Environment (build 1.6.0_26-b03)
Java HotSpot(TM) Client VM (build 20.1-b02, mixed mode, sharing)
Build 1060 (MC: 1.7.3)
No plugins
Using Minecraft-Sheller to run, which uses the command:

Code:

screen -dmS minecraft java -server -Xmx1536M -Xincgc -Djava.net.preferIPv4Stack=true -jar craftbukkit-0.0.1-SNAPSHOT.jar nogui

But have also tried the command outlined in the wiki:

Code:

java -Xincgc -Xmx1G -jar craftbukkit-0.0.1-SNAPSHOT.jar

As mentioned already, I've removed the map completely and had it generate a new one and the problem still persists. Can't connect to the server, can't use any commands to even stop the server safely.

Log dump/Stack trace:

Code:

2011-09-04 11:23:18 [INFO] Starting minecraft server version Beta 1.7.3
2011-09-04 11:23:18 [INFO] Loading properties
2011-09-04 11:23:18 [INFO] Starting Minecraft server on *:25565
2011-09-04 11:23:18 [INFO] This server is running Craftbukkit version git-Bukkit-0.0.0-980-g4ed23b1-b1060jnks (MC: 1.7.3)
2011-09-04 11:23:19 [INFO] MLog clients using java 1.4+ standard logging.
2011-09-04 11:23:19 [INFO] Preparing level "world"
2011-09-04 11:23:20 [SEVERE] java.lang.NullPointerException
2011-09-04 11:23:20 [SEVERE]     at net.minecraft.server.WorldServer.c(WorldServer.java:106)
2011-09-04 11:23:20 [SEVERE]     at net.minecraft.server.World.a(World.java:2078)
2011-09-04 11:23:20 [SEVERE]     at net.minecraft.server.Chunk.addEntities(Chunk.java:470)
2011-09-04 11:23:20 [SEVERE]     at net.minecraft.server.ChunkProviderServer.getChunkAt(ChunkProviderServer.java:79)
2011-09-04 11:23:20 [SEVERE]     at net.minecraft.server.ChunkProviderServer.getOrCreateChunk(ChunkProviderServer.java:118)
2011-09-04 11:23:20 [SEVERE]     at net.minecraft.server.World.getChunkAt(World.java:280)
2011-09-04 11:23:20 [SEVERE]     at net.minecraft.server.World.getTypeId(World.java:227)
2011-09-04 11:23:20 [SEVERE]     at net.minecraft.server.World.isEmpty(World.java:231)
2011-09-04 11:23:20 [SEVERE]     at net.minecraft.server.World.a(World.java:198)
2011-09-04 11:23:20 [SEVERE]     at net.minecraft.server.WorldProviderHell.canSpawn(SourceFile:37)
2011-09-04 11:23:20 [SEVERE]     at net.minecraft.server.World.canSpawn(World.java:98)
2011-09-04 11:23:20 [SEVERE]     at net.minecraft.server.World.c(World.java:186)
2011-09-04 11:23:20 [SEVERE]     at net.minecraft.server.World.<init>(World.java:148)
2011-09-04 11:23:20 [SEVERE]     at net.minecraft.server.WorldServer.<init>(WorldServer.java:27)
2011-09-04 11:23:20 [SEVERE]     at net.minecraft.server.SecondaryWorldServer.<init>(SecondaryWorldServer.java:8)
2011-09-04 11:23:20 [SEVERE]     at net.minecraft.server.MinecraftServer.a(MinecraftServer.java:211)
2011-09-04 11:23:20 [SEVERE]     at net.minecraft.server.MinecraftServer.init(MinecraftServer.java:149)
2011-09-04 11:23:20 [SEVERE]     at net.minecraft.server.MinecraftServer.run(MinecraftServer.java:337)
2011-09-04 11:23:20 [SEVERE]     at net.minecraft.server.ThreadServerApplication.run(SourceFile:422)
2011-09-04 11:23:20 [SEVERE] Unexpected exception
java.lang.NullPointerException
    at net.minecraft.server.WorldServer.c(WorldServer.java:106)
    at net.minecraft.server.World.a(World.java:2078)
    at net.minecraft.server.Chunk.addEntities(Chunk.java:470)
    at net.minecraft.server.ChunkProviderServer.getChunkAt(ChunkProviderServer.java:79)
    at net.minecraft.server.ChunkProviderServer.getOrCreateChunk(ChunkProviderServer.java:118)
    at net.minecraft.server.World.getChunkAt(World.java:280)
    at net.minecraft.server.World.getTypeId(World.java:227)
    at net.minecraft.server.World.isEmpty(World.java:231)
    at net.minecraft.server.World.a(World.java:198)
    at net.minecraft.server.WorldProviderHell.canSpawn(SourceFile:37)
    at net.minecraft.server.World.canSpawn(World.java:98)
    at net.minecraft.server.World.c(World.java:186)
    at net.minecraft.server.World.<init>(World.java:148)
    at net.minecraft.server.WorldServer.<init>(WorldServer.java:27)
    at net.minecraft.server.SecondaryWorldServer.<init>(SecondaryWorldServer.java:8)
    at net.minecraft.server.MinecraftServer.a(MinecraftServer.java:211)
    at net.minecraft.server.MinecraftServer.init(MinecraftServer.java:149)
    at net.minecraft.server.MinecraftServer.run(MinecraftServer.java:337)
    at net.minecraft.server.ThreadServerApplication.run(SourceFile:422)
2011-09-04 11:23:23 [INFO] I'm sorry, Dave, but I cannot let you do that.

 

THANK YOU my friend has this problem! THANK YOU THANK YOU TANK YOU

 

Can both/all three of you try going back to craftbukkit 1000 and see if that fixes the problem?

 

I'm sorry what was the solution? I keep combing through the post but can't find one... What???

 

I don't really know either. However, if you want help please answer a few questions. Version of bukkit, plugins list, and any errors that show up in console.