16B control on a Makino A55E with twin screws on the Z axis. When I jog or command moves the currents on Z and W are well balanced. When I attempt a rapid to reference at a over ride greater then 1% it faults out. It will reference at one percent just very slow. When in rapid reference the current balance is way out. If Z is moving plus the Z current is positive while the W current is negative and quite high. In jog both currents match in level and polarity. Things I've tired, amp swap, synchronization procedure, ran on encoders scales off. Swap out Z motor with new, same, swapped out W motor same. Checked all machine parameters against a backup from a month ago and the only parameters different are 1860, which Fanuc tells me is just a register, and 8900. Neither parameter shows up in the parameter manual so they must be internal use. Feedback devices increment, scales are seeing their zero reference marks.
If I didn't know any better I'd swear the polarity of the motion command to W was reversed but given that they use fiber optics for the communicaiton to the NC that's not possible.