I'm having the exact same issue. I've installed everything as per the directions. FSX is updated with SP1. The Sim Engine Activation Console gives me a green light and states that "Microsoft Flight Simulator X is ready for use with Cygnus" Both the sim connection and cable connected are listed as "connected" yet when I run FSX attached to Garmin Pilot, my location in Garmin Pilot does not reflect what FSX is simulating.
The support from Cygnus has been sparse & of course is only available during "banking hours" Perhaps the Cygnus cable does not play well with an Apple Thunderbolt adapter, although nowhere is this mentioned on their website or in the installation directions. So far, this has been a waste of $200 on a USB cable.