I've already found a major sync instability issue. Download and play back this movie file:
http://dehacked.2y.net/microstorage.php/get/737638915/Pokemon%20Mystery%20Dungeon%20-%20Blue%20Rescue%20Team%20%28USA%29.bk2
Emulator version:
BizHawk_Developer-2020-04-03-230826-#96a753324ada6486d0ec1dd978d0c54e1555a68b
ROM checksum (No-Intro):
File: Pokemon Mystery Dungeon - Blue Rescue Team (USA).nds
CRC-32: b6c4143e
MD5: 61373235da72064e8c058fae3c646916
SHA-1: 503edef4fe6088bca00616efcac3b13da90cd105
SHA-256: 4bdf72ce0dd7a19c66f49e840f046124994d719678e88a0814d0148f705d3e8b
Around frame 640, you will see a Pokémon walking up. The issue is that each time you play back the movie, a different Pokémon will appear! This obviously shouldn't happen in a deterministic environment. Note that DeSmuME doesn't have this issue, as it always spawns the same Pokémon (
Eevee) when it starts from clean SRAM.