I had a similar problem, emulators dont care about the joistick id, they just acept whatever input you give them, some softwares as retroarch or xpadder do care, so if you trying to input joystick 2 buttons but are pressing what retroarch think its another joystick, thats the reason it wont take it. So heres a test you can do, while you want to add the inputs, if the control wont register, just push some of the other controls buttons and see if they showed up. if they do, try finding the correct way to conect your joysticks or controls in the correct order into the usb ports, i often find that the correct order is from bottom to top if you have a 4 usb port on your computer, if you only have 2 ports, you might need to find the way to acomodate 1-3 so windows can assign 1-3 ids. hope i made sence, english is my second lenguage.