How about you back to basics.

Do you have a multimeter?
If so, work out what input on the controller is the E-stop. Then measure the voltage with the E-stop circuit complete (all buttons out and guards in place), and with the E-stop circuit broken (hit an e-stop button). Make a note of the values, then when the fault happens again, measure the voltage at the input. That will tell you if it's a switch/sensor/wiring fault, or a controller fault.

The fact Mach is still communicating with the board and not locking up, tells me it's not an interference problem on the USB side.