AC Servo tuning - Joint 0 following error at high velocities

@andypugh: I checked the coupler, didn't observe any slipping. I too believe that its unlikely to be some encoder issue.

@PCW: I tested with encoder filter on. Still facing the same issue.

My mechanical setup is,

Servo Motor -> Coupler -> BK15 (Two angular contact ball bearing (Back tot Back configuration) with a shim spacer in between ) -> Ball screw -> Ball nut -> Deep groove ball bearing

I doubt whether the issue is due to the ball bearing. I have an electronics background and am just getting started in the mechanical field.
 

I would check the encoder signals at the Mesa card

The way to check is disable the drives (I hope this can be done
in a way the encoders still work) and then measure the differential voltage
(from A to /A and B to /B ) with a voltmeter in all quadrature states.
(you can usually to this by wiggling the motor shaft a bit to get all 4 states)

The absolute value of the differential voltage should always be greater than 2V
(you should get a positive differential voltage in one state and a negative voltage in
the other state)

Another check is to enable quadrature error checking on the encoder and seeing if
you get errors, that is set

hm2_CARD.0.encoder.NN.quad-error-enable
 true in halshow
and monitor
hm2_CARD.0.encoder.NN.quad-error

(CARD is the mesa card name and NN is the encoder number)