Taking a long shot, are you by any chance using the original encoders from the R2E3.We had a BOSS 9 R2E3 (or E4 - not sure which), not all that different from the BOSS 8, with Powertron Servo motors and Contraves encoders. Let me put it as politely as I can after 30 years. THEY SUCKED! The encoders became unreliable after a few months of use and started mis-positioning. Only a little at first, then by whopping amounts, or they sometimes caused a shutdown for no feedback signal. The entire servomotor/encoder setup had to be sent out for very expensive repairs. The entire machine was essentially an abortion that Bridgeport rushed out in order to get one of the first CNC Knee mills with servo motors instead of steppers. After a few years of repeated breakdowns and problems, we had a Centroid retrofit put in that has been highly reliable ever since (with a couple exceptions, but that is not the subject of this post). In the event that your retrofit retained the original servo encoders, I would strongly suggest replacing them. Even if they weren't retained, the encoders could still be the issue..