I’ll have a play with that firmware over the next few days. I’ve certainly produced perfect MM prints with that firmware without any issues. I have a feeling this is only related to manual extrusion, and as you pointed out doubles the extrusion while printing.
Those layer shifts were more likely caused by something else though. The answer is usually pretty clear if you can catch this when it occurs. Ie. you can see if the hotend is flopping around or getting caught on z artefact. Sometimes you’ll hear a clunking sound of a motor skipping steps (insufficient power or bad connections) or opposite, see nothing but notice the x or y motor stop short in either direction (indicating driver shutdown (too much heat. Enclosure fan running?)). It’s now time to go back to those test cubes. When you send pictures I really need to see the cubes from side on and oblique angles.
You don’t have any filament that shoots better than the natural (translucent) stuff you had earlier?
When we’ve got that right, we’ll scale it up maybe 400% and see how the results play out.
While it’s printing. From time to time, put your hand on the x and y motors to ensure they’re not getting hot to leave your hand on. If they are adjust stepper power down a fraction.