Have you deleted all the .cfg files then recreated it as detailed in the link? That has worked for at least 3 others on the forum.
I think there is a conflict somewhere between one or more of the auto config files (that deal with the usbgamepad you have). I could be wrong, but removing them and recreating the one you want seems to work.
RetroPie help guides --> https://goo.gl/Yfy8kj
Please read this before asking for help --> http://goo.gl/eLErnl