Is the first set of mappings exactly as seen in the cfg file? As in, are the #’s there? They shouldn’t be. You have to remove those.

So both sets should probably look the same as what you pasted as working except

input_player2_joypad_index = 1

You can use jstest to figure out which button is which to map to the button in retroarch. But if you say that the uncommented button map works for player 1. Player 2’s should match.