Re: Bad ball screw nut or bad bearings?
I cannot answer your question despite having a VF0 that made the same noise when doing a rapid on the X axis. I hauled off all the covers and tried to identify which it was even using an engine stethoscope without any luck; the noise just seemed to come from everywhere. So I checked positioning and repeatability, and concentricity when doing circular interpolation and everything was fine and within specs. So we limited to rapids to 50% just to cut the noise and used the machine for another three years without any problems.
If your machine is still turning out good parts my advice is to wear ear plugs if the noise bothers you rather than spend several thousand dollars.
An open mind is a virtue...so long as all the common sense has not leaked out.