Load the affected game up once more, and it should again detect your controller. Go back in and uncheck generic game-pad controller support in steam and then return the per-game settings in the effected game to use global settings. Once you have loaded the game and it has detected your controller log back out of the game and return the settings to how they were. Change this setting to Force On and bingo bango the next time you load your game, your controller should be recognized.
Midway down the general tab, you will find the Steam Input Per-Game Setting.
