When a GBA title is launched from anywhere, the system completely closes the actual 3DS firmware, sends the system into GBA mode, and then loads the game from your sysNAND titles into RAM. So, if you launch it from emuNAND without having it on sysNAND, you're basically just sending it into GBA mode without giving it anything to launch, which is where the error comes from.
Installing it on sysNAND should fix the problem. If it doesn't, there's a few probable reasons:
It's a fluke. Launch it from sysNAND first and see if that works. Then try emuNAND.
There's something wrong with the ROM used to make the cia file.
The cia has a bad footer (basically rom metadata; it could be reporting wrong save type, rom size, etc). This usually just prevents saving from working properly, but it's possible.
Your CFW doesn't support GBA cias.
AGB_FIRM is missing/corrupt/not patched (note that not all CFWs require you to patch it).
The cia wasn't installed properly (unlikely).
Hope this helps.