Right now Emerald can be played using gbarunner2 on the DSi and 3DS, and DS only in rom3m branch. This is because the DS has less RAM than the other systems (if I have understood correctly). You are running your DSi with only DS capabilities, which makes you lose out on a lot, like improved audio and running more games.
Answers. From what you've said, it sounds like Emerald is faulty somehow as other games appear to work correctly. The first thing to do is to check the contacts on the cartridge. If they're dirty or damaged then this will prevent the game from loading properly. The fact that the GBA is stopping on the "Gameboy" screen suggests that it isn't
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can you play pokemon emerald on nintendo switch