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.