I've seen behaviour like this caused by a dodgy USB device. A random process would spike and if you killed that, another one would spike in it's place. This was under windows XP. I tracked down the offending device by systematically removing things till the problem went away. Once it was removed there were no further problems. I'm guessing it was windows I/O system not coping well with the hardware problem.
Similarly, try going through any other things that might have changed around the time you started seeing the problem. The device in question also caused problems under Linux.