Dave,
We have lots of folks using this with EFIS systems, autopilots, fuel computers, etc. No reason it won't work with your system too.
The data is sent on Pin 3, trying Pin 2 would not serve a purpose. In fact connecting Pin 2 could make the connection more flaky. The iFly employs a sort of smart-switching system for the USB port. When you connect something it tries to detect the stream of data to figure out what to do with it. If there is no data, or it doesn't recognize the data, it allows the port to be used for as an NMEA output. We had one customer who connected the entire 9pins to his efis system, and there was some sort of data pump coming from that system which was confusing the switch, and the iFly would never configure the port for use as an NMEA output. He cut Pin 2 on the cable, then everything worked fine.
Because Alasdair actually sees the NMEA settings dialog when he goes to Setup / NMEA Output (which I've presumed from his first post), I know the port has been correctly detected and allocated within the iFly. I'm confident the data is being sent; I believe the problem is either the cable or the connection. One way or another, we'll get it fixed.
-Walter