Hmm, seems to work fine with the SDL port. Looking into the Qt one now.

E] Can reproduce, Qt port is broken.

Seems like Pokémon Yellow asks for 2-controller mode, then increments which controller it's asking for 8 times (which goes back to the first controller) and since it sees it's the first controller again assumes it's not a SGB...

I think this might be a timing issue. I think it swaps the controller every frame, but it takes too many frames and winds up being an even number of frames (8) instead of an odd number (5 in BGB unless I miscounted).

Bumping this up just to point out that the base Japanese rom (Pocket Monsters: Pikachu) has no trouble whatsoever with Super Game Boy enhancements. Borders and color work perfectly. It seems that every revision and regional release that followed is affected by the bug.

MapleStoryPSN, that could have something to do with the first Japanese version having no Game Boy Color support.

Pokemon Yellow was sold as a regular Game Boy game in all regions. But it had Game Boy Color features anyway. The first Japanese version was older, seemingly too early to get the GBC features. They added the GBC support in the 1.1 version. All other regional versions were based on the Japanese 1.1 or newer. This makes me think the problem might have SOMETHING to do with the GBC support. But I'm certainly no expert.

There's a byte/some bytes in the header that tells the GBC when the game has GBC support, but I don't remember where.

No, I don't think that's related. Though I'm not sure what the problem is yet.

Any new development on this issue? I noticed the same thing yesterday. Some Tetris game has the same problem, I believe Tetris 2.a

This is the relevant code, which is identical to the code in Pokémon Red except for the sending of the MLT_REQ packets, which are shielded by di in Red. (Yellow sets the variable that prevents joypad polling in the caller function instead.)