Certain SNES games and emulator combinations have issues with the controls, e.g. certain versions of Super Mario: One solution in those cases is to switch to player two. With that controls you can continue to play then. That is not an issue of the ControlBlock.
Generally: If the controller works in one program, but not in another, then it is a matter of configuration of the specific program. The ControlBlock is working correctly then.
Hope that helps!