Electronics for New Machine + Chinese Spindle + VFD

[JAZZCNC]

I did notice that the case (which is earthed) may of been touching the outside metal part of the USB connector. I fixed this and plugged the USB in again and it then connection was established ok. Not sure this is related to be honest.

Yes this would cause problems because it would create an earth loop with the PC. The USB gets it ground from the PC earth.
Don't earth the case of the PC to same Star Earth point used for the control box. The Pc gets it's earth from the Mains directly thru the plug.

Vibration or resonance won't cause these problems. It mostly makes the motors run rough and lower performance not miss steps etc unless really bad.

USB can be flaky to start with so if you have any poor wiring connections or noise going on then it will be picked up.

But Before starting on the wiring I'd go over the mechanicals with fine tooth comb to make sure no lose couplers or binding issues.

Then Go over your wire connections very carefully. Make sure Power wires are away from signals. Esp around the VFD.

Trying to diagnose problems like this is difficult from distance because it could be so many things. Often it's something really simple or silly.!!