Kicking it would have been my first choice But it seems that didn't work.
Mark the mechanical parts (couplings, shafts, etc) with a Sharpie. That way you can see if anything is slipping. Then look for any mechanical binding in the system that might cause you to lose steps. Does it only do this when cutting parts? Try an air cut to see if you are getting the same problem, use the Sharpie again to put witness marks on the Y axis to see if the stopping points are the same. Is the position repeatable when jogging?
It really sounds like a mechanical problem, software doesn't change overnight.