I recently had this same problem with Y motor error. I would get random Y position error alarms and then it started becoming constant. I talked to Graphtec and they said replace the motor, but they don' sell it anymore. But I have seemed to have solved the problem and the machine works 100% now.
The problem with the Y motor lies within the encoder. This is on the bottom of the motor and one gold screw is holding the cover on. When you take the cover off you will find a glass disc connected to the center shaft. This disc is read by an optical sensor. I had very small dust particles on the encoder disc. I slowly and patiently and softly cleaned the disc with Q tips. I used a magnifying glass to see a little closer than normal. After cleaning the disc and putting everything back together the machine works perfectly now.
I hope this helps everyone with the mysterious Y position error.