Well, everything I was about to suggest concerned mechanical backlash, but since you’ve ruled that out …
Somewhere in the X axis drive, there is a loose setscrew allowing a shaft to turn just a little bit. For example, here’s a hard-fought problem that came down to 1/6 turn of a setscrew:
Everybody believes their problem can’t possibly be a mechanical problem. However, when the configuration hasn’t changed, that’s a clue the problem has nothing to do with the configuration.
