So this sounds like something that happened to my friend. He had 2 of the same gamepad the problem was that when we went to input and changed the input to another device, the name didn't change therefore we weren't sure that it was even reading both seperately. We fixed it by taking what we considered p1, moving the device name in the emulators input config to the far left, and configured our buttons. Now when we went to set up player 2 we started far left then clicked one to the right. The name didn't change but it did in fact pick the other controller. We then set up accordingly.
