Not sure....but they're are a lot of unique colors loaded total. If you have too many, it might mess up some other palettes... I did something similar when I changed the 'little kids'(beating up Glenn) to each have different colored hair.
They worked together, but I'm not sure about Sprites that are involved in battle. Just out of curiosity, try using different colors (even if they look bad)...JUST to see if this is the case. Perhaps you can find a more suitable configuration.
Yeah, ROMhacking is *definitely* about getting around what doesn't work they way you want, you might even find something cooler!
~Z