@dc42 I think the issue is finally solved! I may have had multiple issues, because I'm still not sure why this would affect homing direction, but you were correct, I had a wire on one of my two z axis motors that was hanging by a thread, sometimes not hanging at all. Because my issue appeared to be X/Y related I never took a real close look at the Z axis, I finally caught an error message about motor/driver 2 and phase, I realized the Z axis gets triggered to lift the head off the bed even for X/Y calibration.
Thanks for the help, everyone, the fact no one saw any issues with my firmware config and the wise men thought motor issues, that changed my target and enabled me to spot this unknown bad wire.
Thanks again!