Ah, you mentioned an IP/M, and it sounded as if you were having the same problems with that. A friend of mine recently bought a Chinese router that uses the XHC controller. AFAIK, he is using the latest version of Mach3 with the XHC driver that came with the machine, and that is all working fine. I know that he homes each axis in turn, though. The only homing issue was discovering that one of the proximity switch targets was badly adjusted so the machine hit its end stop before the switch. That's when we discovered that the target was a broken tap screwed into a roughly drilled hole, but it did have a locknut! Quick tweak and all was fine.

If you are satisfied that your machine is solid and beyond reproach, that's good. Mine is all-welded steel but the mounting plate for the switches could be a source of vibration, and there is around 50um backlash in the ballnut/ballscrew assembly, as far as I can measure. That's enough to go between on and off and back again with my switches. I'm glad I went with the IP/M from the outset, although even that has its little firmware oddities, as it lets me work around the issues.