From the "stab in the dark" department;

I just started a thread on grounding that you may want to follow. Grounding and also shielding are apparently serious considerations in CNC.

One example in my experience was the Z axis motor randomly bumping a step while it was stopped. It was located adjacent to the variable speed controller which was in the original plastic box. After reading that these controllers can be very noisy electrically, I moved the controller and associated switches and relays into a separate metal box located off the machine. All that goes to the spindle is the 120v dc power feed from the controller box.

So far, that seems to have cured that problem.

could be earth leakage, that held me up for a while. It takes very little current to ground a pin. Use a seperate supply like a 'phone charger, feeding your estop and limits, and use it to hold a relay closed. Wire the relay contacts to your logic pins.