Craig, Davek0974, thank you both for helping.
I'm also skeptical about Mach 3 having such a bug, its been around for long, and why would it show-up after a year of regular operation on the same rig, a dedicated PC that receives MINIMAL maintenance and changes.
Vdc and I at PSU seem OK. Motor couplers OK. Temp of one axis a bit high, to my taste.
Monitoring pulse trains on a 4 channel scope, pretty boring pattern, using its memory to keep as much data as possible. Figuring out a way to have the scope halt acquisition after a failure.