I've had this irritating problem lately. Whenever I play Quake 3 online (seems to not happen offline). I have 10 fps drops about every 10 seconds or so. I've disabled pretty much everything (especially punkbuster). My PC is very fast and only seems to be happening after a recent clean install.

Edit: I have also tried messing with which CPU core and the process priority Quake 3 is running on.