No problem, I'm glad you got some of the games working properly for you.
I went into the input test in service mode for SkullGirls and my controls work properly there, but in game, player 2 up = player 1 button 2, player 2 down = player 1 button 3, player 2 left = player 1 button 1 and player 2 buttons 5/6 = player 1 second character specials. Frustrating! Perhaps the game itself has these buttons mapped out and fixed when running. I will try some different combinations.
I tested out Contra Evolution Revolution and had the same control issues in game. There might even be more games with control problems, has anyone else tested this?