Or at least it camw with FFTPatcher 0.478.
Problem: whenever you try to export portrait and click corresponding palette for portrait it still gives you a messed up portrait when you open in Paint.
I tried the old Shishi from .352 and it works perfectly.
that's because paint will try to use the first 16 colors to do the whole sheet, shishi's and the game automatically use the 8th row of colors for the portrait area.
You will have to use GraphicsGale if memory serves me right in this. That way you can see the palettes and switch them at (relative) will.