Hum ... following on...

If restarting Mach3 after one job solves the problem, how about hitting the eStop after one job and then the Reset? That fires off the sdame Init string. Does that sort out the problem?

If so, I would look very closely at what M codes you have at the end and how they interact with the wiring around the eStop line. A mis-wiring around there could be the problem. Yes, I am definitely looking for a HW problem here.

Cheers