I’ve never used the SE but I doubt there’s really any difference with the non-SE. This is not related to FlightDeck either.
Could it be that the SE is a EU version? In this case, you may need to flash an FCC firmware onto the internal radio, hoping that the antenna is compatible with the frequency (not sure). It may also then be advisable to flash the RX tot he latest firmware as well.
It could also be that the TX and RX are too close during the binding process (usually not as much of an issue for binding specifically, unless really next to each other).