I'm assuming you're using the unofficial English patch, king? Given the nature of it, I'm wondering if the unaltered build has the same bug, or if the palette swapping is being caused by the patch code.
If you've got the time, try messing around with it and see if you can pinpoint some specifics. Is it just the size of the lead Pokémon, or some other factor that's contributing to it, like species or type? Is every building at risk of the bug, or just the Mimic Girls house?
Thanks for posting this. Most intriguing. It'll suck if this turns out to be part of the game's main code.

FaFniR: The PokéNerd in me thinks it would have been better to keep Surf for the Pikachu, I think. It's a great way of dealing with Ground types that it would ordinarily be at a disadvantage against. Fly is a hard move to use properly, because it takes two turns to execute. It usually has to be paired with a move or ability, like Mean Look or (Toxic) Spikes, that will prevent or discourage switching out to a Pokémon that's resistant to Flying-type attacks on the next turn.
Whatever floats your boat though. If you're having fun with it, that's the most important thing. Besides, most of the NPCs in Pokémon games aren't
usually that crafty.
Hi! I like shorts! They're comfy and easy to wear!
You're not wearing shorts! What's wrong with you?
Silly Youngsters.
