if you set it up at either the GLOBAL or Game specific, and it registers correctly then you should have no problem. The only thing that i could think of is that you might be mistakenly taking how the games works. Lets say PACMAN for instance, even thou you setup the second player controls, its not going to use the second player control, it will only use the ONE player controls for both players. Alot of alternating game does this. Now if it don't work on a 2 player simutamously like a Neogeo fighting game (kof97), then you have problems, but then again you said it registers when you set it up in the Game sepecific section.