I might be overlooking something terribly, but how do you set controller buttons and axis? I open the input menu, go to flight, and hit the grey buttons with the arrows. There it says Current Assignment: None. I move the appropriate axis, see the text change to Current Assignment: joy0.1 and confirm by clicking Accept. I open the same menu again, and my axis is unassigned again. This is confirmed in-game, with KSP not reacting to my controller inputs at all.
What is going on there? How do I set my buttons and axis so that I can use them in-game. I am currently using the 64 bit version of KSP.