A quick summary:
When you run the same job and get randomly different results, it’s a mechanical problem.
It looks like you’ve eliminated quite a few mechanical problems and corrected several mis-calibrations, but there remains (at least) one more mechanical problem.
The hardest part of debugging, at least for me, is when I’ve checked something and decided it’s OK, but overlooked a detail. At that point, I know the problem must lie elsewhere, so I’ll look everywhere else for the longest time.
Now that you’ve eliminated the obvious problems, start from the beginning and examine everything again. Other folks have discovered how subtle the problem may be:
- Invisibly loosening screws
- Excessively small stepper driver steps
- A bad USB cable
- Bad assembly at the factory
- Loose focus lens (or a mirror)
- Loose motor screws
The point is, look carefully at all the places you know can’t be the problem …