Obvioulsy this will depend on your answer to Gerrys question, but you may want to try un-shielded cable on the y-axis encoder. Sometimes the shied can cause a problem you haven't thought of.
Only other thing I would try would be to either switch off the other two drives and see if it makes a difference, or physically remove the other two motors from the machine to see the effect. Does sound like noise, I have had a similar problem recently.
EDIT - Oops, you are using steppers, sorry my bad!
(Note: The opinions expressed in this post are my own and are not necessarily those of CNCzone and its management)