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Which emulator are you referencing? Do both controllers work on NES games? I have a feeling I just posted the answer to this question. I was having the same issues, but both controllers worked fine on NES games but doing what you are describing on SNES games. Turns out the problem was the SNES emulator that RetroPie uses by default. Here is the fix. https://www.petrockblock.com/forums/topic/2-player-snes-issues/