If you updated the retro-pie script this may be the issue:

Error with RetroPie Setup scripts

If you go in this directory and type ls -lah
/opt/retropie/emulators/RetroArch/configs/

do you see a file that has been updated recently?

Here is a working combination:

Working controller config files attached

Or as you say, pasting a valid button config direct into the retroarcg.cfg file in opt/retropie/configs/all should work