Pony Fantasy VI Remake

"Frig. I jinxed it. Sombra entering the Sealed Gate, looks screwy. I'll have a look at that thread."

Yeah, damn that map, and a handful of others. Unfortunately, there's not too much that can be done to solve it, without some sacrifice.
The gate doorway is being colored by a 'modify background palette' command in the entrance event (event the map uses at all times), so it is coloring all objects/npcs that are palette 6 on that map no matter what, characters included. It's quite a b*t*h to work around. I had to just let it happen on some of the more important maps that need to keep the modified palette command in the entrance event, while other's, like Zozo, I was able to just remove the object that was being modified (the crane) and the command as well then. One of my main characters is palette 6, I'd imagine in your case it will be much easier to deal with since it's just Banon and Gestahl, as you said.

As for that particular map, though... I can't really think of what to do except maybe temporarily have gestahl there (that's Samba right?) use a different palette if another one looks decent enough, that or remove the gateway NPC there and the entrance event command. Come to think of it, I had the same issue with my palette 6 getahl on that map... It's when they open it already, after Thamasa? I had to make a duplicate Sealed Gate map on one of the unused maps, and obviously did not include the modify object palette command in the entrance event. I think that's what I did anyway.

I'm still wishing someday someone will be able to find a legit workaround for this issue, to free up palette 6.