Uhh, pay no attention to my last comment...
It's happening again.
It only seems to be happening with the characters that share the same palette.
I really don't think it should be doing this. Is it possible there's a timing or mapper glitch in MMC1?
I've defragged my memory card and everything, so I don't think that's it.
Actually, I noticed that I don't get the bug when using my older NES. My r11 board gives this problem, but I have one with the r7 board, and there's no problem at all. Neither of my systems have mods (besides the lockout chip, expansion sound mod, and the r10 one has a blue LED instead of a red one).
My everdrive:
The 72-pin NES n8
a 4gb SDHC card
My NES:
Original North American Front loader. uses the rev11 board.
My other NES:
Original North American Front Loader with rev7 board.
My (broken) nes:
NES-101 Top-loader, USA, circa 1993.