Homing (wiring) seems backwards

I’ve found my machine sometimes loses it’s mind and inverts or confuses all the axis’ movement. Seems to happen have long job maneuvers… but I’ve had it just power-on confused too. Only solution I’ve found has been to dump my settings via serial ($$), connect with carbide motion, do a “send config”, the push all my dumped settings back in. Been a while since that’s been needed though…