I'd probably mess with the acceleration some more. Although it's counter intuitive it's possible increasing the acceleration will help.
Does the motor act the same way at any part of the table?
- sorry, I know you already said binding isn't an issue, I just figured I'd ask this anyway in case it helps.
Maybe something is wrong with that driver?
Try hooking the Y to another driver - does the problem go away?
Hook the Y driver to another axis - does the problem appear on the other axis?