Hi Steve,
Yes there have been a few problems with the Aerofly connector. Like you said it comes with a stereo connector on the interface which can cause problems with some of the newer JR transmitters. There's alot of info on the net on this rather simple fix to be honest. Alot of guys just bridged the two L/R tabs inside the little connecter with some solder or even a tiny wire to convert the connector to mono. Of course the negative is a single connection so it's only the rear two tabs that needs to be connected.
The other alternative was to simply grab a female stereo connector and a mono male and built a little converter with two wires.
Cheers,
Rudolf