I have been playing some fighting games the last few days and have been wondering why the switching players in games like xmen vs street fighter or marvel vs capcom wasn't working and why I couldn't do raging demon with Akuma. I believe I figured it out, it seems that when I use the controller setup and get the prompt for "Top 2" it is actually setting that button to Fierce Punch" and when I get the prompt for "Top 3" is is setting that button to "Strong Punch".

I don't know how to fix it, I just press the buttons in a different order and now the arcade controls are like I remember them from years ago.