Does it run long enough to compare the speeds on the Motion Info screen? If motor Encoder speed doesn’t match command speed there may be a drive parameter wrong. Check drive parameters 558 and 609. 12” gov should be 240 ppr, 16” should be 320. Did you do the velocity command adjustment when you put in the new MSU? I think there is a motor RPM adjustment in Motion adjust and make sure Jog is 100.