I think your solution is found in the setup guide for the NES30 controllers:
http://forum.8bitdo.com/thread-328-1-1.html
I had the same problem, till I followed the setup to the letter. You need to configure the controller twice. Once for the dpad first, then a second time for the remaining keys.
<quote>
reboot your raspberry pi
While loading hold start on your controller to turn it back on
your blue light should go solid when you get into emulation station
it should ask to setup a controller. ( if not use the a usb keyboard hit enter to open the options and config controller)
Hold down on the Dpad (it should say keyboard)
Only set UP, DOWN, LEFT, RIGHT
Skip A, B, START, SELECT, LEFT BUMPER, RIGHT BUMPER
then hit ok
Now reopen the controller config and hold A (should say 8Bitdo NES30 GamePad)
skip UP,DOWN, LEFT, RIGHT ( you should be able to use your down arrow on your Dpad to skip them)
Set A, B, START, SELECT, LEFT BUMPER, RIGHT BUMPER
then hit ok and you should have a working controller.
</quote>
