I have an odd problem I’m hoping you can help with.
In my super nes emulator the player 2 remote only works if there is a button pressed on the player 1 remote (any button). This is true in games like Bomber man 1,2 and Donkey Kong Country where both remotes are active at the same time, but sometimes the player 1 is not playing. Games like Mario which are turn based don’t have a problem.
I am having the same issue along with a couple of others: terrible lag and the Pi being slow to recognize the controller (PS3 over USB). In my research today, the suggested reason for the “other” issues was lack of power over the USB ports. It dawned on me that it was suggested to get a 2 amp power supply, but I had a 1 amp one laying around so I used it. I have seen similar problems before with other electronics and underpowered adapters so it does seem possible. What is the rating on yours?
It might be worth looking into a different SNES emulator as well. I had issues with 2 player on the default pocketsnes emulator so I updated my setup script and installed the lr-snes9x-next emulator and I didn’t have any issues after that. See this video for a step by step: