Hello,
i have the same problem here, with version 3 beta 4.
Ok, i have this Pad http://www.pcstats.com/articleview.cfm?articleid=2096&page=2
I can make the configuration in retropi and also use it in emulationstation.
But if i start nes oder snes (didn’t tried any thing else yet) it only works a button like shooting ore jumping.
I can still use the keyboard config.
Regards
Wicht