(this is taken from a thread i made on my priv twitter, so i'm copy/pasting here so the full thing can be put together)
1. randomization of the rom
im going to assume y'all are familiar with pokemon randomization. we all kinda know about it. change up what pokemon you encounter, your starters, all kinds of shit. 'course, in order to do this, the randomizer (or whatever method you use) fucks with the rom to some degree
and that includes stripping it of its AP (anti-piracy) patches.
roms themselves usually have AP patches on them, so theyre able to run without AP measures being taken. i.e, you can play pokemon without the game just shitting itself and being unplayable
"wait, but i've randomized a rom and played it on desmume and it works fine! why would stripping the AP patches be a huge deal then if it just works fine with emulators?"
well, that's because not every emulator is equal.
2. twilight menu++ the emulator(?)
..twilight menu does not actually emulate.
"what the fuck does that mean isnt it an emulator"
it doesnt emulate, by technicality. yes, its an emulator, but its not one at the same time.
it runs nds-bootstrap, which runs games in the native DS bios. this is perfect for it, since, y'kno, its an emulator meant for DS roms on a 3DS. running roms natively, with their patches and all, as if it was an actual DS game on a 3DS bios-y shit is perfect for authenticity
unfortunately, this means that twilight menu is one of those emulators not made equal.
thing is. when emulating a game, and you fuck with the rom and accidentally strip the AP patch, no big deal. emulator compensates for it. but, lets say you do the same for nds-bootstrap...
3. pokemon black randomizer (from 2 povs)
the game is unplayable.
i cant gain exp. my game crashes if i try to catch some pokemon. my fight button disappears. i am forced to go into the n fight with a lvl 5 scolipede and lvl 2 wailord. this went badly. restart. same thing.
however, nene's playing the same randomizer seed as me. why is her game running much smoother?
well, it's kiiind of. hers crashes not as often, but she still gains exp. her fight button still disappears though.
she got to gym 5 or 6 before the game just went down, same way as me
now hers crashes when she catches pokemon, and she no longer gains exp. it just took a bit to kick in, i suppose
...anyways randomizing pokemon black is what made me look into this to see if there was a fix, and that's how i ended up figuring out how this shit all works.
(small disclaimer: i am not a tech or emulator pro, this is just what i've gathered from looking around at people who initially had the same problem.)
(there is also a technical fix: patching the rom again after randomizing it. however, it takes a bit more time, but i do wanna try it out. maybe i'll report back or somethin' if i find out it works well.)