I'm having a similar issue. I have a Thrustmaster T16000M and I can see it in my controllers section and I can choose a profile to map to it, but when I try to use it nothing works. Also, if I try to manually set keybinds the game doesn't seem to recognize the input. I've tried installing new drivers, switching USB ports, modifying registry, etc.
I'm running an i5 3570k, GTX 1080, 16GB RAM and Windows 10 Anniversary edition.