Did you figure out what was causing this problem?
I'm also having the problem, but with Diablo III. After a fresh reboot (even a warm reboot), the game works perfectly, but over time (several hours), I'll get the problem where the game runs too fast and becomes very choppy. This only gets worse over time until I have to reboot to make it playable again. If I leave the game completely, and then load it up again, the problem is still there. Doesn't matter if other apps are running in the background or not.
I also use a VMWare virtual machine to do some work at home, and when I'm having this problem, the clock in the VM runs way too faster. The clock will count 60 seconds in maybe 10 seconds of real time. I cannot even double click on items on the desktop in the vm because the two clicks are not happening fast enough since the vm pc clock is running so fast it doesn't register the event as a double click. Yet if I reboot and load up the vm, it works perfectly.... but after a few hours it gradually gets into that situation again.
I did a clear reinstall of Windows xp and reinstalled all the programs that I normally use and I started having the problem again. I did not notice if this problem happened on the clean install but before all the other programs were reloaded so I cannot rule out program interference but I don't think that is the case because I used msconfig and disabled just about everything that was non-critical.
I'm beginning to wonder if there's some timing chip or something on my motherboard that's getting wonky. For reference, this is an older pc using a dfi lanparty nv+ with an amd x2 4400 processor and 2 gig memory and I'm running xp sp3 32bit. Video card and hard drive have been replaced and the problem still happens.
Any thoughts?