Controller not working when loading ROMs

[TkSilver]

My guess is that you have a game specific setting saved for the game where the controller stops working and the controller in that game specific setting is not set up correctly (either not set at all or the controller changed from controller 1 to controller 2 or 0 or 3 or something else silly).

Press triangle over the game you can't get the controller to work in and edit the game's specific settings from the menu that pops up. Hopefully that is the answer. The same thing happened to me one day and it took me 2 hours to figure out what was happening.