Jollyroger,
I have found and solved the issue as far as my system is concerned. This is what it was:
I also had a Microsoft Rumblepad game controller installed on my machine. It was selected as the default controller for older programs. I changed this default to my transmitter, and I also calibrated the transmitter in windows first, before going back into FMS and repeating the calibration procedure.
Steps:
1) Go to Control Panel, then Hardware, then Game Controllers
2) Select your transmitter, and click advanced.
3) Select your transmitter as the preferred device and click ok.
4) double click on your transmitter
5) select the settings tab and then the calibrate button.
6) complete this calibration procedure. There will be a few points that you cannot complete (like pressing a button) ignore these and click next to skip them.
7) Click OK and then OK again to close the dialogue boxes.
start FMS, and go through the cal process again.
You should find that it is now responsive.
Good Luck!!!!