Just FYI, got tired of dealing with Mach 3 and installed an Arduino between the parallel port and the 540, with a homing program connected to the switches and it works perfectly now. I can post the program if people want to see, lessons learned here were that Mach does control direction outputs and override the Arduino even if there is no movement, so you would either have to disable those outputs from Mach in software or disconnect the cable while using the Arduino homing program. A $10 solution.