Author is going to need exact step-by-step reproduction documentation to figure this out. A save state immediately prior (say within 10 seconds or so), followed by exact and very clear instructions on how to achieve it, is necessary. Without that, I can assure you rdanbrook will prioritise that ticket extremely low (I know I would).
To me though, it looks like more "oh great, more of THIS crap" PPU nonsense, as in going to take a ton of man hours just to figure out what's going on. There's a whole series of graphical corruption that happens (meaning it's not just a palette thing), so for all I know it could be a timing-sensitive thing, or some $2002/$2005/$2006/$2007 read/write ordering quirk.
Reminder to folks: Nestopia plays, oh I don't know, ~97% of all games reliably, so please keep that in mind. All that ever gets reported these days are edge cases. I think that's worth taking into consideration / remembering. Same goes for many of the
other major emulators.