Ok then its not so bad as you can at least still use things. As I mentioned earlier this was an issue with the SmoothStepper in the early testing of it and was seen, if I recall, if you had the kernel set to anything other than 25KHz. Might be worth trying different kernel settings in Mach and restarting to see if any correct the reporting issue. As the pulsing is done externally in the PoKeys changing the kernel will not, or at least should not, affect motion.
Failing that helping then I am afraid you will just have to press NeaTO for some action.
Hood