I know i'm a month late but can you simply not download the .cia file instead of the .gba? It will be directly added to your 3ds home menu so it'll be a much more smooth experience for you since you won't have to go through TM++ to launch the game. And GBARunner2 is frankly kinda crap.
Just use FBI to install the .cia and play it directly. And if you need to grab the save file just use Checkpoint.
At the time I was specifically trying to run it on a DSi XL, not a 3DS. I haven't personally run into any other issues with GBARunner2 but admittedly I haven't tested it out deeply either. I didn't realize there were so many holes in the compatibility list, knowing that makes this issue make a bit more sense. lol. I have other systems I can load this on though so it's not a huge deal to me, just thought it was worth noting.
