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Mike:

Half and full step are known to lose steps more easily when under load.
Mach2 does pretty good with them, but not as good as Dos. This is because
the pulse stream of Mach2 while very stable does have phase distortion as a
function of its algorithm. This doesn't affect microsteppers but full and
half steps can be affected unless the driver is very well matched to the
stepper motor.
Its a good thing you have a workaround as this can be very difficult
to track down and fix. Does this happen in Exact Stop or only CV modes??

Thanks,
Art
www.artofcnc.ca