All three motors on my Taig mill now have a slight random hesitation since replacing a crashed Vista PC with a newer Win 7 PC. The hesitation happens both in jogging and cutting air. The sound is not quite as strong as the “clunk” when switching on the Gecko G540 controller. I believe all the settings are identical with the ones I’ve been using for several years. Except for the PC, the hardware is identical with the old system. I've played with the settings with no change in the hesitation. Has anyone had experience with this? Any suggestions to diagnose the problem?

Sounds like you have a lot of jitter in your parallel port output. Have you tried running the driver test?