I'm having similar problems. Mine is doing the greying out thing. It did it the first time I started the game (no mods). I was able to set one axis at the time, every time I set a axis I had to restart the game. After a few restarts it went to windowed for some reason and let me finish setting all my controls. Today after I broke my stand alone throttle. I needed to reassign a few axises and it will not let me set a throttle axis at all. Now it greys out every time no matter what I do. O, all the mods I have is MechJeb and Fuel Tanks Plus