A couple of times recently I have noticed that 'something' is causing the Windows System Process to sit at 50+% and it will not quit until the PC is rebooted. Happening on Win2k and Win XP so far.
This is particularly troublesome because it currently appears to be triggered by MSVC 2005/Incredibuild and rebooting the build servers is not a nice thing.
At the same time the 'System Idle Process' process is holding the rest of the CPU and the build steps themselves seem to be starved. ie. a module that normally takes <5 minutes to compile is currently taking 20+.
I'd take a few guesses at maybe being virus checker or tortoise svn but would desperatly like some other suggestions.
Edit:
I've been experiencing this as something that is triggered, and the culprit may not be ongoing. Thats not to say that some other ongoing process hasn't done something 'stupid' and is managing an active lock up of System while appearing to be idle itself.
System (100% of 1 core), and System Idle Process are sharing 98-100% of the total CPU. Occasionaly mt.exe, link.exe, buildservice would get a look in at 1-2%. I'm running VNC to view the machine, so it's getting a look in on occasion.
Edit 2: When left the previous evening the build process seemed to be progressing all be it slowly, but after waiting another 13 hours the 1 hour build process hasn't completed. System is still hogging the 1 core.