If your hitting the jog keys and Mach thinks it`s moving but the machine only moves sometimes its got to be primary computer issue unless all 3 drives are intermittent on the machine.

Had similar issues at one point, things I learned.

Mach likes living on its own on a blank , just vanilla xp, non internet connected machine, no screensavers , no virus checker, nothing. Use a USB key to load files.

Some paralell settings are buried in the host PC`s bios.

USB hubs are the spawn of the devil on a Mach machine, just keyboard and mouse and port for a memory key, had usb hub that would randomly tug computers arm anything from 20mins to 2 hours into a cut and Mach would lose its place.

Running the Mach test exe that checks the timings is well worth doing.

Its easy to get checkbox blindness in ports and pins settings, have another look after a break.

Nothing has had a 5V paralell port in years, usually 3.3V, BOB will need the USB to 2.1mm D.C. jack to get 5V to function reliably.

Adding a 3rd axis is a lot more confusing that you think it will be coming from plotters... ;-)