Grr same problem here, I built my own arcade controls and it used to use an i-pac, a keyboard encoder but because SF4 does not let you have keyboard buttons for the 2nd player I had to totally re-do my setup with a new encoder. I used 2x Chtulhu MC boards and now my arcade controles show up as gamepads in windows. Start button for me is Button 10, no matter what I do my controles wont save when I configure them and no matter what button I push when it says "press start for 2nd player" none of them work, I tried every single button!

I have spent more money on my controls to make them work for the game than I did the game itself! Capcom your game team needs to fix the SF4 control options fast!