I'm guessing its really related to a crappy controller/build. I am guessing that something happens to make the machine pause and then it raises the torch. The plasma cutter you have is a good one. I have the same one.
The first thing I would look at is noise. Find the Hypertherm grounding document, add a star ground point and run seperate earth cables back to it from every motor frame and make sure wires bridge over any linear rails. Then add an EMI filter to the control box. If that does not work, I would suggest you consider upgrading to Linuxcnc Plasmac configuration, but get the grounding right first.