Hi Judleroy!
Well it definitely appears to be an encoder position measurement problem. A motor or amplifier problem can not cause such a problem. A bad motor or amplifier would cause the motor to not move or move too much and then the DRO would be way off. Either the encoder itself, the wiring, noise, or the KMotion encoder input are possibilities to cause a position measurement problem. From the way you describe it sounds like the quadrature counts just drop out for a while. If you were to plot the Commanded and measured Position on the Step Response Screen if you see "flat line" conditions where the encoder suddenly stops changing for a while that would be a big clue. Sometimes the encoder read head alignment for is very marginal such that it works ok under no load (when turning by hand), but under torque it goes out of alignment. A simple test would be to swap the x and y axis motor/encoders to see
if the problem moves with the physical encoder. Or yes you can use amplifier #3 (instead of #1) and encoder input #3 (instead of #1). Just move the wiring and change the input and output channels for axis #1 (Y) from 1 to 3.
Regards
TK