One interesting possibility is a failing DIP switch on the stepper driver. You’d (well, I’d) swear such a thing couldn’t happen, but we had exactly that situation come through a while ago:
Changing from 2000 to 2500 is a factor of 25%, which is exactly what would happen if SW5 failed open on (for example) a DM542A driver: the step/rev setting changes from 4000 to 5000.
Ponder the table on the side of your driver to see if a single switch failure could add 25% to whatever the settings call for.
Once is happenstance. Yours might be the “twice” making it coincidence. If somebody else has it happen, then it’s definitely enemy action. 