At his point, send the machine back to zero, and see if it actually goes there (Sounds like it will not).if I cut : bottom left, top left, top right, bottom right then the two right hand holes are approx 5/6mm too high.
If not, check everything mechanical first. Make sure everything moves smoothly, with no binding. Make sure everything is lubricated that needs to be.
If it's not mechanical, than it gets into electrical issues, which are much more difficult to troubleshoot.
But if it's repeatable, I'd say that it's more likely to be a mechanical issue.