I know this sounds obvious - and is possibly stupid (too lazy to check the HRM at the moment and find out
) but my guess would be that the games that the second button doesn't work on don't perform the same check in their code for a press of that second button as the games that it does work on...
Edit: To clarify, what I mean is: Is there only one standard defined signal that can come from the joyports that should be regarded as "second joytick button has been pressed"