I have one machine that uses a 5 meter LPT cable without any issues but I would not want to use a USB cable any longer than say 1 meter. Extending cables is generally not good practice but if they are of good quality with gold plated pin and socket connections then it should not be a problem.
Just as a test try reducing the Velocity and Acceleration of your Y axis in motor tuning by 50%, saving the changes. Does it now still have the problem ?
Tweakie.