Pokefirered: editing type interface icons messes up colors

No matter what sprite editing tutorial I use or what program I use (graphicsgale, photoshop, and at one point i got desperate and used mspaint to see if that would work), when I edit the icon spritesheet for pokemon types, the colors are in reverse order from what they should be on the index. I've even tried to reverse the index, invert the colors on the sheet, and so on with graphicsgale and nothing works. Also, when I save the sheet with graphicsgale, the compiler will throw this error:
I've also tried editing the .pal file that comes with it, but that ends up changing the colors for the rest of the interface, which I'd rather not do.
What am I doing wrong, and how can I fix it?