Huh that's weird. I don't think note colours should affect it, but I guess it might be worth trying without them if that's the only thing you're doing differently.
Are you sure there's no double notes? As in are you sure there's not a 2nd B2 in the same space?
Also, are there tempo changes? They can sometimes be fine, but they will often cause issues.
No overlapping notes, no tempo changes, though surprisingly it WAS the note colors, I changed them all to be the same (while changing nothing else) and it worked lmao. I do remember having to import a midi once and the colors were saved, I guess it makes some extra data that gets read by the game in a weird way?
before and after for reference in case that matters:
Huh I guess the colour index must be stored in the same byte the timing data is in? And my code doesn't handle that because I never considered that, because like, why would it work like that lmao? Idk when I'll get around to fixing that, so yeah I guess just leave it at the default colour, I've added it to the doc.