High Precision Event Timer (HPET)

couldn't remember the name to save my life...had to boot the dinosaur to look for it in the BIOS. Listed under Power Management on mine, but it could be elsewhere in other systems (if it's an option). May just be an on/off option, or you may see 32/64-bit options. Obviously, don't use 64-bit if you have 32-bit Windows. 32-Bit should be safe for anything from XP forward, but you might have to get updated chipset drivers from your manufacturer if it doesn't auto install them. It should show up in Windows under System Devices in Device Manager if it is already using it.

Not saying it's the root of your problem, or your ultimate solution. But in theory, it may smooth things out a bit as it was designed to help streams synchronize better. It's a much higher resolution clock than the older RTC method. Think of it like clocking racers using the second hand on an old wrist watch versus using a stopwatch that can break it down into hundredths of a second. The much tighter intervals provide closer gaps in the clock cycle to more accurately synch multiple streams.

Ultimately though, it may call for a driver fix. If you've recently changed drivers, it might be worth rolling back to see if it resolves things. If you've recently installed new hardware, that may be supect too. USB and IR devices have been known to do weird things with other games in the past--something as seemingly innocuous as a new game controller could be behaving badly if it is using a custom driver or some sort of button management service that runs in the background.

Just spit-balling here...trying to jog your memory to see if maybe you've overlooked a recent change to the system that you might be able to undo.