As of beta 8 there is still a desynchronisation between the PSG ("beeper") channels and the Direct Sound channels in Pokémon GBA games. It doesn't only exist after loading a saved state; it builds up over time, an additional desynchronisation of 1 second per 15 minutes or so, until you reset the emulator. This started happening when I raised the output frequency to 65536 Hz, which I did to make Golden Sun 2 and the GBA Video cartridges not sound like Tay Zonday.
I've tried multiple solutions to fix the sync in Pokémon while keeping the games that needed 65536 Hz audio working. Either:
* in all games using Direct Sound, the sound runs twice too fast for 0.5 second, silences for another 0.5, twice too fast for another 0.5, silences for another 0.5, etc.;
* in all games using Direct Sound, the sound becomes 8 to 32 times too loud, like an electric guitar being used by a newbie who doesn't know how to set distortion;
* in all games, the sound pops loudly 16 times per second -- even if that sound is actually silence (!);
* all games except GBA Video cartridges and Golden Sun 2 work, but GBA Video and Golden Sun 2 emit no sound at all, or just static, or just crackling.
This has to do with hardcoded assumptions that the output would always be at 32768 Hz. The code has no way to represent a single clock cycle (1/16777216 of the GBA clock speed) being partially rendered at 65536 Hz, so the Direct Sound timing slowly drifts away.
So, I present you guys with a choice. Do you want Golden Sun 2 and GBA Video to sound nice, or do you want the music in Pokémon GBA games to be synchronised? It can't be both.