Most likely this was due to a corrupt .xml file.

Make a copy of it asap, and next time you experience any type of strangeness, delete the .xml in the Mach3 folder and replace it with the backup copy. Much easier than doing a clean install.

I've had my .xml file go bad twice in the last 18 months. In both cases, the machine would no longer home. It would move a fixed amount away from the switch and stop, every time. I don't know if anything else was affected, as I didn't run the machine, since I couldn't home it.