It may sound strange but you may want to try wiggling the wires attached to your steppers while it is moving around. If you hear it skip steps while you are touching the wires then you may have an issue with the wiring moving during the jobs. If the connection to the steppers is loose enough to compromise the circuit then they can skip. If you find this to be the case then you could find better ways to secure the wires.
I had this happen to me once on a Davinci 2 3D printer. The wire harness was zip tied to an anchor point but there was still a few micrometers of movement at the connection and that was enough to cause random skipped steps in either direction. I looped the wire harness and zip tied it twice and the problem was solved.
Since the steppers move around on these machines and the wires have to move with them I worry that may be an issue on occasion.