Hey Philip,
Did it stop in the middle of the way?
If so, it could be point 5) in this document. When the controller is powered off, can you move the Y rails freely, with no noise?
And when you move it into the three mm gap, do you feel any resistance?
It could also be possible if you get a current interruption in one Y stepper cable connector that the one Y axis moves some steps while the other not, and at a certain degree of disalignment, the machine would block. With these flimsy connectors, I always suspect an electric problem 
See point 3) in this document.
Anyway I would first try what Mike suggested.