In the system I found there is a accumulating positive shift after each axis movement that doesn‘t show up on the DRO‘s.
Does this lost position happen on every axis or only one? Logic says that it must be one of two things.
First is mechanical slippage. Somewhere between the stepper shaft and the axis.
Second is lost steps on the stepper. This can be mechanical load being beyond the steppers capability. Maybe a tight spot. Maybe acceleration and or rapid too fast.
What stepper motors, driver, power supply are you using? Are you using a break out board?
After ruling out mechanical issues cut the acceleration and rapid speed in half and see if that makes a difference.
Greg