One fix worked for me: Exit the logitech profiler. It worked then.
Flight stick is Logitech Extreme 3d Pro. Game detects inputs while in the game itself, but not in the menus while trying to remap Z-axis to yaw and X to roll, like it should be.
I have the same controller, but buttons 2-5 and 10 don't work
I'm running dual Thrustmaster T1600Ms and have the same issue. Swapped USB ports and that actually changed which axis woudn't map on the same controller. Hopped over to Elite: Dangerous just to be sure, and everything worked fine there.
Edit: got it working through luck, more or less. Just kept switching USB ports until the axis I needed to map detected input in the menu.
