i had similar problems maybe this could help:

instead of this:
cd RetroPie/emulators/RetroArch/tools
./retroarch-joyconfig >> ~/RetroPie/configs/all/retroarch.cfg

try this:
cd RetroPie/emulators/RetroArch/tools
./retroarch-joyconfig >> ~/RetroPie/configs/all/cf1.cfg

it will create a textfile called cf1.cfg, open it and copy all the content (mark it, rightclick, copy).
now open the retroarch.cfg file in you /all folder and overwrite the similar lines that are already inside this file with your copied content from cf1.cfg.
(mark old content, rightclick, paste new content)

sounds not very elegant, but for me it works, seems like were doing something wrong, so the controllerconfig-program cant save directly in retroarch.cfg.