The game froze on me (big surprise, right?) during the end of the tutorial. I reloaded my last save, but the game wouldn't recognize my Dual Shock 3's right stick. I tried turning off the controller, restarting the game, rebooting the system and using other controllers, all to no avail. I eventually had to restart from the Doc's house because of it. It worked perfectly from then on, but losing my first two hours of gameplay was a headache.

Im having a similar issue except my two joysticks are swapped and there is nothing in the settings to switch them to what they are supposed to be. My LS is to look and the RS is to move. The game isnt playable like this at all

I had this problem a couple of times on FO3 - I corrected the problem by connecting my controller to the PS3 with the USB cable.