It may be you have dirty glass on the encoder. If you take off the little cover, you should be able to clean the glass with a cotton bud.
Try to slow the rapids to see if the fault improves.
Set up the amps as follows (assuming you have a BX 0.0001" control):
Start by powering up the servos and winding the gain pot CW until the axis oscillates, then wind it back until the oscillation stops plus a further three turns.
Wind the Tach. pot fully CW then back eight turns. wind the Sig. pot fully CW then back about five turns. Put your meter on DC volts and measure the voltage at the brown and orange wires on the edge of the amp being checked (or between pins 8 & 9 on the relevant channel on the servo board).
Jog the axis forward and backwards at 25IPM and adjust the Sig. pot for 0.65v in both directions (use the Bal. pot to even things up about centre i.e 0.64v one way and 0.66v the other can be balanced to get 0.65v both directions).
If there is not enough adjustment on the Sig. pot, wind the Tach. pot CW one turn and try again. When you have 0.65v in both directions, wind the Gan. pot CW until the axis just becomes unstable then back it off 3 turns.