It could be an issue with the gantry not being properly parallel to the rails. Because of the design it easily for one side to get a little ahead of another when the machine is powered down.
One forum poster has some set blocks he uses to make sure the y axis is properly aligned on startup.
Another poster had a homing switch mod that also did this:
A mod to protect limit switches:
You may want to talk with someone who has upgraded to the XControler. As it has each y motor on a separate driver chip so they are no longer tied together.
Because you are running as such high accelerations you might want to look at other controllers. It might make a difference for your application. (I am not sure as Acceleration and Torque curves are still pretty confusing to me.)
GRBL does linear acceleration curves.
TinlyG does S acceleration curves.
I believe the smoothie board does S curve acceleration too.