I have seen a very similar problem to this on my DFP when trying to change mappings (gears to stick from default paddles) - don't know exactly what caused it - the game behaves as if your pressing the ESC key - so you don't get a chance to remap the key, very, very frustrating seeing that window pop up and not even getting time to read it..
I think its to do with confusing the game, by switching to desktop and opening/changing settings in Logitech Profilier whilst still in Game, and then changing mappings in game.
It could also be to do with the order you start everything in - when the game first starts, its as though it checks whats there and what it will recognise, if my wheel is not setup and calibrated BEFORE I start the game I have noticed problems when trying to remap buttons, its the same with headtracking if its not running before the game starts the game will not recognise it without a restart.