UPDATE: I have a mistake in my original post. On the gamepad adapter, the right port is player one and only THAT controller connected will work in a game. the player two port will not work in a game, but both controllers will work in EmulationStation.
Any help would be appreciated, including any personal InputAutoCfg.ini file from someone who has the same setup and has both controllers working. I’ve tried messing around with that InputAutoCfg.ini file, but have been unsuccessful. Thanks in advance!