If Z is moving around 25 times further than required then the motor tuning for the Z axis is probably incorrect, it is most likely doing exactly what it has been told to do.

Make sure tuning is correct may be totally different to X & Y and be sure to save axis settings every time changes are made, you solved the motor tuning problem with auto calibration in this or previous thread, how are you measuring that movement accurately with much smaller Z axis movement any errors may be larger.