is your hd activity light coming on during these short breaks in the gameplay?
maybe a far shot, but its happened before that some program running in the background which is accessing the hd every second or 2 and freezes everything else...
so my suggestion would be to fire up msconfig, (start > run: msconfig) go along to the last tab called "startup" and disable everything except driver apps etc (like the ATI Tray app).
after you do that, restart and see if its made any differences, if it has, you'll know its a program that you have on automatic startup, which narrows it down immensely.