First and last time I ever saw a problem like this was on a i845 machine with a Celeron 1.7GHz. It really killed that machine. Task Manager didn't really help as you've possibly found. Sysinternals Process Explorer was need to show it was interrupts.

Solution to that was a new motherboard. Probably not what you wanted to hear. That sounds like quite a new and expensive machine. That's basically the specs of our brand spankers Win2k3 file server.

My theory was that the mobo was simply generating random spurious interrupts. The OS would spend heaps of time blocking etc to service them, find out there was nothing there and then return to normal.