I see this is a very old post, hope you got it fixed...
Is the machine closed loop (encoder or Glass Scale)
Servo or stepper ??
If it is Stepper it is probably open loop, it is most likely losing steps check for excess drag on Y axis. You may need to slow the acceleration rate to fix.
If it is Servo closed loop, check that there is no slippage between the encoder and ballscrew. Check for lose electrical connections and/or noise on encoder signals.
If you got it fixed what was to problem ???
I am having similar problems on a big Vertical Machining center with the Z axis losing position about 0.020" over 4 to 6 hrs of running a program (production)
I am rewiring the Z axis encoder with new shielded cable and going to see if that fixes it.