Try this, decrease your accel and velocity on one of the troubled axis to 25% of what it is now. Run the same file before and after this adjusment and let us know if the error is the same amount. As far as your steps per being right, do the math to get to that if you can. That will eliminate a lot of guessing, If you measure it your assuming you have not skipped any steps and often backlash isn't accounted for (depending on how you have been measuring).

Brett