I am having an issue I have seen mentioned here many times without much of a clear answer,

Where ? I haven't seen this mentioned so frequently here. One thing that beginners are stumbling is the fact that only the P1 controller is able to run the hotkey enabled actions, but situations like P2 not working at all, that's not something that's reported.

To start, I configure both controllers in the Emulationstation UI. I have also configured both controllers in RetroArch UI and saved the profiles. I have done that step both from the RetroPie menu and on the fly from the game with a Rom loaded.

There's no need to re-configure the controllers in RetroArch if they've been configured in EmulationStation, the latter will take care of properly configuring the controllers for RetroArch.

Once the game starts however, I have no luck getting inputs from the controller on Port 2

Is this a 2 players game and you've chosen to start with 2 players ? Which game it is ? Does this happen for other systems also (PS1/NES/etc) ? Did you change the 'Device type' in the 2nd Port to something else from the RetroArch's ?

@sleve_mcdichael You are THE BEST!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! I am so embarrassingly ignorant. I have spent 2 weeks trying to fix this and it was just the order I plugged the buttons into the controller? AAAAUUUUGGGGGGG!!!! Thankfully I can (and frequently do) laugh at myself;)

Thank you again!!

Rob

@pietdummie quick menu > controls > port 2 controls > mapped port:1 should map the gamepad in port 2 to port 1, so that either one will work. (I don't know what happens when you press "start" on P2, though. Does it work as 2P start, or does it read as P1 input and just start 1P? You'll have to test...)