100% CPU usage... does anyone else get this?

Here is my code. I would have simplidied it for you... but I honestly have no idea where it went wrong.
One second it is running fine, the next it starts taking up 100% of my CPU cycles. I can't figure out what I did to it to make it do this... nothing I added creates an infinite loop or infinite threads. It's just... weird.
The code is probably too big for anyone to look at and tell me what's wrong, but can someone else download it and tell me if you also get 100% CPU usage? It needs to be run on Windows... it uses a couple JNI calls that are Windows-specific. Those calls were the first place I looked when trying to find the problem, but I have not changed that part of the code for a long time, and it has never been a problem before.
Don't run the bat file... just navigate to the Watchdog2 directory and do 'java Watchdog'.
Are there any tools that can help me figure out where the program is getting hung up? It's not freezing at any specific spot... just moving super slow and taking up 100% of my CPU. I'm so confused...
Message was edited by:
L4E_WakaMol-King

Nevermind!
Sorry for the trouble. The problem was that last time I compiled the code, it reverted back to and older version of a class I had compiled days ago. Why it did this is totally beyond me... but it did, and it just so happens that the old version of that class combined with the new version of my program were the perfect recipe for an infinite loop.
Seriously, if you are in inveterate debugger, you might get a good laugh out of this. I've spent the last week and a half trying to find a way to set the Windows console into cbreak mode (single character processing rather than line-at-a-time processing), and I finally managed to do it by writing some c code and putting it into a DLL with the JNI. So now my program (which runs from the console) can process each character as it is entered rather than waiting for a line return. The older version of the class that got reverted was one that used System.in rather than the input stream generated by the socket. I had set it to System.in for testing purposes, and apparently that testing version is the one it got reverted back to. So combine the two, and you have a console that is feeding System.in each character as it is pressed and a socket wrapper that is listening infinitely. It was a mess... but an uncannily serindipitous mess...
Ahh... debugging... good time...

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