Ok, so I figured everything out. First; I followed the first part of the guide at this location:
For getting RetroArch’s keys to match up with the gamepad controls. However, I think my problem was that I had the same key command mapped for Quit RetroArch and Menu
So, for future reference for anyone else having this problem, here’s how to fix it:
- Boot up retroarch on your gameshell
- Navigate to Settings->Input->Input Hotkey Binds
- Map “Menu Toggle” to whatever key(s) you want to bring up the emulator menu with
- Map “Quit Retroarch” to whatever key(s) you want to return to the GS menu
- Boot up mGBA under the emulators menu
- Press whatever button you set as “Menu Toggle”
- Go to controls and remap as desired
- Happy gaming!