When I first ran the game, I set the controller config using the wizard and the game ran fine. It seems however, that every consequent time I run the game the controller config hasn't been saved (I can move up and down the main menu but the buttons have been un-mapped, btw I'm using a Logitech F310) and I have to re-configure it every time. Has anyone else had this problem? If so is there a way to get the game to permanently save the controller scheme?

Edit:

Well, I ended up finding out the solution to my problem (so I'll leave the question up). The way to make sure the controller scheme is saved is to go through the Joystick Calibration Wizard from start to finish, and then start the entire process again before you close the game.

When I ran the wizard a second time (just to see what was going on), I realized that the way the buttons were mapped changed (e.g. For the 'Run' command, the current was set to [2+] and the default was [X], probably the game assuming an xbox 360 controller). When I exited and restarted the game, the controller scheme was still in effect.