Sprites in Palette, Indexed, but legs are color-inverse.
So I've been working on respriting Ivan's Space Marine mod to Black Legion Chaos Marines, and it seems to be going alright, but I've run into a problem. The legs gave me a lot of trouble when I was trying to put them in palette, but I finally got it by indexing them to the Cortex Command palette in GIMP. Now there aren't any more artifacts or invisibility, but the colors are inverted, as seen below.
Did I not palette/index it properly? Is there something else wrong with it?