Hello there!
I know you said the machine was tight, but it sounds like a backlash problem.
A repetition test wouldn't pick this up.
My favourite way of testing backlash is to set Mach to a fine jog increment (eg .001mm or 1 thou ). Then jog an axis up against a dial indicator until it moves a bit. Zero your Mach DRO, then fine jog the reverse direction until the dial indicator starts to move again. The number in the DRO is then your backlash measurement.
I am a bit wary of calibration routines. If you know your lead screw pitch, stepper driver microsteps and any driver gearing due to belts etc, you should be able to calculate what the steps per unit should be. If this is different to what the calibration routines give there might be a problem somewhere.
I hope you get it sorted. Good luck!
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