The key question is will it go back to zero. The second key question is if it is coming out short of the destination point or past it.
I have seen the taper locks on the axis get loose and slip, especially in rapid.
I have seen encoders get loose from the motor shaft. Both would cause a failure to return to start point. And probably a failure to get to the destination.
A bad encoder or loose encoder can create a situation where the machine may overshoot because it does not see enough counting pulses. A bad encoder can still return to the start point.
Just things to check.
George
(Note: The opinions expressed in this post are my own and are not necessarily those of CNCzone and its management)