The step pulses are generated by software, in a very low-level driver. Anything in the system that loads the CPU, or the memory busses, can prevent that driver from issuing the pulses exactly when it should. Video drivers, network drivers, and other high-bandwidth devices can do this. On-board graphics controllers can be particularly bad, since they generally keep the frame buffer in main memory, so can significanrly increase latency of CPU accesses to memory. Get the Windows optimization instructions from the Artsoft website. That will give you a good idea the kinds of things that can affect pulse stability.
Regards,
Ray L.