Many applications use DirectInput, which Joy2Key is not entirely compatible with under all OS's.
1) Map your inputs to the native gamepad controls, not keyboard keys.
2) Try using RBjoy. It seems to be able to handle DirectInput better, but be aware that it is a layered solution. It will send the keycode you want it to, but does not block the system from sensing a button press. If you have both the key and the button defined for different things, they will both be activated.
3) See #1
RandyT