YOu're on the right track re; motor tune.
Assuming you're encoders are proper count, you may have a motor that has a different response curve than machine was initially programmed for.
Also, you need to have the motor tach's checked. IF it is an SEM, the tach's can go flakey after a while. Clarkson near Chicago can take care of them (factory service center).
Brian at BPT Machine in carol Stream ILL tuned my "trak and did a superb job (630-784-9942). Fixed a bunch or other "issues" that I was living with in the process. I have no affiliationn with BPT and paid the bill like anyone else would have to.
Backlash and lead comp are issues he took care of as part of the tune-up as well as gibb adjustment check....