The glass is bolted on to the mechanism via 2 plastic brackets which are bonded onto the glass - it may be that one of the brackets has come unstuck and as a result the glass will tilt when trying to put the window up and as soon as it feels resistence it will stop.
Panel is easy to remove - 2 screws in grab handle, couple down the sides, couple underneath, and there should be 1 behind a plastic cap on the door release handle.