To be honest, i think the current layout of retroarch.cfg is just a huge clusterf*ck. I couldn’t get the same thing running. Until i found another gamepad config at /opt/retropie/emulators/retroarch/retroarch.cfg and /opt/retropie/emulators/retroarch/configs/yourcontrollername.cfg

In the end i removed all controller references from /opt/retropie/emulators/retroarch/retroarch.cfg and /opt/retropie/configs/all/retroarch.cfg and edited NintendoWiimote.cfg (your config might have another name). After that, i finally got this running the way it should.