Sorry to bump an old thread, but for others reading this I feel I should clarify what happened here.
In actual fact Mach3 wasn't doing what the GCode told it to do. There was a glitch somewhere in the OS. The toolpath window would show a toolpath that did not follow the provided GCode. X would suddenly flip negative for no reason whatsoever- not a single negative X value in the file...
The solution for him was to format the hard drive, reload windows and the Mach3 software. Nothing short of this seemed to help.
Thanks,
Chris