It would be very helpful to connect up a computer with PronterFace on it. Put the nozzle in the center of the bed and give it an M119 command. You should see everything untriggered. Click the 'Motors off' button and move the bed to the home position where you would expect the Y-Axis endstop to be triggered. Do another M119. It should be triggered.
Is that what happens on your machine?
Is that what happens on your machine?