Support Request: My server was working flawlessly and then blew up. [SMP 1.1]

I have a SMP server with a few of my friends. Everything was working perfectly. We were busy exploring, building reactor and odd contraption when suddenly the server become MASSIVELY unstable. It was in the time of Minecraft 1.1. I also had a buildcraft mod and redpower with it.
The strangest of things is really that everything was fine then it seem to have corrupted itself. Ive tried looking around but no one seem to have quite the same bug.

Error log:

[IC2] BuildCraft integration module loaded
Exception in thread “AWT-EventQueue-0″ java.lang.NullPointerException
at lb.a(SourceFile:42)
at lb.a(SourceFile:12)
at lw.actionPerformed(SourceFile:30)
at javax.swing.Timer.fireActionPerformed(Unknown Source)
at javax.swing.Timer$DoPostEvent.run(Unknown Source)
at java.awt.event.InvocationEvent.dispatch(Unknown Source)
at java.awt.EventQueue.dispatchEventImpl(Unknown Source)
at java.awt.EventQueue.access$000(Unknown Source)
at java.awt.EventQueue$1.run(Unknown Source)
at java.awt.EventQueue$1.run(Unknown Source)
at java.security.AccessController.doPrivileged(Native Method)
at java.security.AccessControlContext$1.doIntersectionPrivilege(Unknown
Source)
at java.awt.EventQueue.dispatchEvent(Unknown Source)
at java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown Source)
at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source)
at java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown Source)
at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
at java.awt.EventDispatchThread.run(Unknown Source)
[INFO] Starting minecraft server version 1.1
[WARNING] Can’t keep up! Did the system time change, or is t
he server overloaded?

and then the server just keep spamming the warning time change.

I tried updating everything to 1.2.3 but the problem seem to follow with the world folder. Its interesting because some chunk possess the mods block and its working fine but some other chunks, everything mod related is remove and lag like hell. So after banging my head on the keyboard, the screen and the mouse I humble request assistance in this matter. If someone could point in a direction to fix this to avoid the lost of all our work I would be eternally grateful.

DeathZero34

I know the warning is concerning the refresh rate of the graphic but its always there, even if there are no players in the server. Which is even odd because if no one is in the server, why would it need to refresh the graphic?

I'm more concern about the AWT-EventQueue-0. Ever since that showed up some of the chunks are broken (mod block wont even show on those chunks) while others are fine. Those chunks are also plague by INTENSE lag not your regular lag that slow you down, its crippling. (I know it doesn't make much sense).

I don't believe its spec oriented because I'm sporting an i7-970 at 3.8Ghz and a good graphic card. I also host the server on a different computer that never lagged before.

Quote from RichardG

That error is a bug within the server's GUI that can be ignored.

Time changes happen when the server is too slow to keep up with the world, but talking on that and the lag you're having, it's usually not a wise idea to run a server and a client on the same computer unless you have a pretty decent computer.

Does anyone know a tool that would allow only some chuncks to load or to check chunks integrity?

That a good idea but would'n such a thing still show the pipes and the carries and stuff? The block that were from mods disappear on those "corrupted" chunks. I also did an experiment for the hell of it. I took MCedit and deleted the entire chunks that show the problem and it seem to have at least fix the lag.

maybe the warning and the Exception in thread “AWT-EventQueue-0″ are not has related as I though they would be.