I'm having the same problem where none of my controllers are working in game, however, I know what you're talking about, as I had that same thing (with the having to basically hold all the buttons to get it to open the remap screen) happen to me. Unfortunately, I have no idea what caused it, and I was only able to fix it by doing a clean install. If it's any consolation, since the install I haven't had that problem (just my current one where my controllers aren't working in game)