Mach 3 with large Gcode files can cause inconsistent problems resulting in lost steps. With a 1/16 bit with large stepover can produce a lot of lines of gcode and thought possibly this could be your problem. I spent days trouble shooting and turned out just shutting off display was the simple fix.

I use 2010 screenset and there's a button on top of screen. Not sure for other screensets.

Good luck
Dan