Disklavier

Hi all, so I have a customer with an upright MX100IIXG that I somewhat recently replaced the LED light circuit board on. I have to admit first off that I did not perform calibration as at the time I was not trained in how to do so and could not get a hold of the manual in time. Lame excuse, but anyway. Since then, the original problem of certain notes not being registered by the customer’s computer has been fixed, but now he is complaining that there is a latency on only certain notes and only some of the time. I have spoke with Yamaha already and they suggested to run calibration and make sure the piano is regulated. (Can’t remember how regulation was last time I was there) My question for everyone here is, does anyone know what setting in Protools the customer might have to adjust in order to correct this IF it is a problem with his program or MIDI setup? He mentioned that he’s never had any problem with MIDI connection in the past. His studio tech also said that everything looks good on the technical side. I’d just like to know if anyone else has encountered this problem and I’d like to be as prepared as possible going in. 
Thank you!!!
Michael