If you want to use regambox with usb gamepads and you don't like the default setting you can modify it here.
This mode shutdowns the pi2jamma control key demon pikeyd. Now the control interface is free and other hardware like pi2scart addon can be used. Default mode is automatic. This means the attached hardware is recognised automatically. Turn explicit settings if you know what hardware you are using (no, this is not self evident :)) and save 3 seconds boot up time.
Take this option and select from a list of pre configured USB pads like snes usb pads, xbox360, c64 mini joystick and more.
Use this opion for lr-fbalpha. The default setting put fire button 1 to arcade control panel button 4. Correct, if you now have a 3 button panel you can not play any game. Use this option then.
Simple tool to check your buttons.