Let me repeat my previous question - do you have a system override where the RetroArch settings are different for the gba system ? Is your gba system's configuration file custom/different from the default that RetroPie installs ?
Post the config file (/opt/retropie/configs/gba/retroarch.cfg) on pastebin.com. If you can, get a verbose log from RetroArch during this occurence and post it also on pastebin.com