The thread you linked is actually using nintendo's Virtual Console software, which does have a GBA emulator in it [albeit a slow crap one] but it was never used for GBA officially as far as I know, instead, nintendo's official method for playing GBA games involves rebooting the 3DS into a special firmware that's sole purpose is to run GBA on the console.
Unfortunately the VC in that thread is not the same as the one you are using to play GBA games at proper full speed and everything.
When you play GBA roms the regular way, you are rebooting into AGB firm, and are using a special mode of the 3DS, not an emulator, as such, what you are trying to do in all likelihood is completely impossible, at least for the time being.