I'm not really sure what's going on here, and it's going to be a bit hard to help you without looking at the sprite.
What I can tell you is that you have to make sure that your sprite has no more than 16 colors in its palette, and that the very first color of said palette is the same color that you decided to use as the background color of your sprite, because that's the color that the GBA will interpret as a transparent color.
Also, you have to make sure that your Litten's front and back sprite both use the exact same palette. Same order of colors and everything.
You'll want the regular sprites of Litten, its front and back, to use Litten's normal colors, and similarly, the shiny palette has to be properly compatible with both, the front and the sprite.