But I think the RPM on the screen comes from the spindle position coder and not from the spindle motor pulse generator.
There are actually approx 4 high pitched noises per motor revolution, not 1/rev like I wrote at first. It is not exactly 4 noises per rev though as I marked the pulse generator gear as a visual marker. If the marker coincide with one noise it will sync up with the fifth noise and the 9th, but then slowly drift out of sync, so I dont think it is linked to the 4 poles of the motor. This also shows it is not linked to one area of the pulse generator gear as it drifts. If I remove the spindle V-belts the noise is still there but much less pronounced. I think the motor is not turning at a fixed speed but more of a pulsed speed. The noise seems triggered to either acceleration or deceleration. If I run from MDI at 10 rpm the RPM on the screen fluctuates between 10 and 16 rpm.

I am reading some generic VFD trouble shooting guides from other manufacturers and it does not seem like a good thing when output voltage or current is not even between the legs. Unless Fanuc drives are unique in that unbalance is normal I would think something is wrong with my drive. Specially since running the motor direct from mains at least shows the same current draw on each phase.

If someone could point me to areas of the drive to check it would be great.

Andy