Agreed, check the motor for knocking noises off load.
Also, using the Drivemonitor trace function, you can observe very closely what is happening in the drive. You can monitor the encoder feedback, the drive setpoint, the actual speed and then you can see if the torques are swinging wildly and causing rotor knock.
Another thing to check which most people take for granted is the motor shaft / encoder coupling, this can slip if it is a non standard coupling. If however, it is a taper fitting, then this is unlikely.
There are 10 types of people . . .
Those who understand Binary, and those who don't.