Disclaimer: I am not a Fanuc tech, so my suggestions should be taken in the general sense only...
If possible, I'd have a look at the control input signals going to the drive to see if it's being commanded wrong. I'd also have a look for cracked solder joints.
I don't know how your spindle drive is commanded; but if it's +/- 10v analog; an intermittent connection somewhere in the chain (not necessarily in the wiring) could conceivably cause this behavior.
Also - you could be aware of this, but I'm going to leave it here just in case (or for anybody else who reads this):