If you go to the Hardware keys settings and configure keys for PAD2, FPse will sense the keys and successfully bind them. However, when I start a game (in this case Mortal Kombat Trilogy) and try pressing the keys for PAD2 something goes wrong. The game seems to register when a key is pressed down, but not when it is released. Hence, when you have pressed a couple of buttons nothing more happens, since the game thinks all buttons are pressed.
I am using FPse 0.10.48