Modding shiny sprites pokémon BW and BW2

[uncrested_emperor]

So, KazoWAR (the goat) made a tool that makes it supposedly easier to insert new sprites/texture changes to gen5. I have been using it (BWSE 2.2a) to change some shiny sprites, following his rules where no color can be the same as the original, max 16 colors, correct dimensions for the sprites etc... I am having one major problem tho: Whenever I edit a shiny sprite, the regular sprite also gets edited to some random colors? 

I can't for the life of me figure out how that happens. Even when I make it so the background is a different color. 

it still syncs the non-shiny color to something random. If I try readding the regular form how it's supposed to be, my custom shiny changes with it.

Anyone know what to do? What I am doing wrong? Better ways to edit shinies?