Ok. All change with the pins again 
The only thing I can suggest at the moment, without detailed information about the sensors, is that you ensure there is no direct optical path between the LED and the pick-up device. Ensure that the light from the LED can only get to the pick-up device by reflection from an external object. If necessary create a small hood from card to go over the pick-up device to limit the direction it can receive light from.
Ian