I know there was a problem with some computers/motherboards losing clock ticks with 2K/XP, but MS released a fix for that. I am assuming you have all the XP updates.
The only other thing I can think of is possibly something causing the CPU to be too busy to catch the clock ticks, even though it is the highest priority interrupt (next to NMI), it is possible to lose those ticks when the CPU is overloaded.