Can you elaborate on the particular key bindings you are using?
It does not matter at all...
After it changed back to default, I start the game, go to settings and change one button only (lets say, forward, to a random another key), accept it then just quit the game and start again, it is on default again.
It's like it doesn't save settings at all.
This problem is limited to control settings, video settings are saved (increased antialiasing to 8x)...