If the copy of Mach3 came with the machine, is it a genuine licensed copy? There are quite a lot of "pre-licensed" copies around and they are notorious for giving weird results and inexplicable problems. One possibility is to download a genuine demo copy of Mach3, use your existing configuration files, and test to see if that works. Demo versions are limited in the length of gcode they can run but are otherwise fully functional so that would see if there is a Mach3 problem or not.