Ok, so I've used this program called JoyToKey several times to map my keyboard and mouse to my PS2 and Nyko Playpad for other games like Minecraft. Essentially, you can set any keyboard press and mouse movement to your controllers. It doesn't override the auto mapping of 3DNes but if the controller is not working, then you can use this. Also useful if you want to make your controller rotate the screen with a analog stick or anything as a matter of fact. Very useful and I've tested it with the Nyko Playpad.
JoyToKey's Website: http://joytokey.net/en/download *100% Free* (Unless you want to buy a license if you like it a lot.)
If you have any questions let me know.