I have done a fresh image install of retropie 3.2 and configured my gamepad on initial boot onto EmulationStation. The gamepad works perfectly in EmulationStation, but as soon as I load an NES ROM the D-Pad does not work in game, but other buttons work as expected. I have tried removing the config file through SSH and rebuilding using the retropie_setup.sh script. No change.
I have tried multiple ROMs in multiple emulators, all have the same problem.