Try it by moving up on teh table in Y about about 2-3" from where you started originally. It could be a stiction problem on tha table at that point OR it could be a controller problem OR you are right on the verge of loosing steps on teh Y axis config setup (Vel,acel) Try reducing teh Vel and Accel settings by 50% and rerun the Gcode.
Have you tried it with different Drill cycles ? G81 , G83, G73 ? I would all 3 to see IF it made a difference. Also I would try a manually programed cycle to help rule out some things.