When assigning commands to buttons on a controller through the options interface at least some of the options activate when you press the button to apply it to the desired command. For instance, changing a button that is currently set to turbo will cause your ship if you are docked to turbo. This happens with weapons fire and some menu options.

In the past I have ignored this as it usually allows the change to occur or I change it in the file itself. I'm posting this today because while trying to set up my game pad with the options I like to have easy access to, I find that one of the default buttons is set to bring up the mission board. When I use the button to apply it to the function that I want, it brings up the mission board and the usual confirmation 'blah blah yes or no want to do this'. In this case after multiple attempts, the setting will not change. Normally when this happens, I go into the wgaf file and either specifically assign the option I want there or set it to nothing and then make the change in game.

When in game settings, button presses should be divorced from the game.

ahhhhh.
Are you using Android?
Android handles controller buttons differently than PC.

I'm currently on a pc running Windows 7. Before that I played on XP. I don't remember if I had this problem when I was on Ubuntu.

I tried playing on my phone once and said to heck with that.