The same problem as me,just yesterday after I update OS 0.3 and use the gameshell-setup，include the RetroArch update.
Anyway,I think you can try to cover the RetroArch’s retroarch.cfg by tool,for example
the WinSCP. HERE it’s my file,and it’s works fine on my GS.
the file location is:
/home/cpi/.config/retroarch
hope to help