Does anyone know what would cause this texture issue in Pokemon ORAS? (Anime Sceptile Rework)

[Airist]

So I've been working on an anime retexture for the Treecko line, and for some reason, I just cannot get the eyes to work. The eye textures are the same exact color as the body textures, and I've included Ohana3DS images to prove it. Does ANYONE know how to fix this? I'd be happy to share my files if you'd like to use them(assuming we fix the issue.)

So what's really weird is the Sceptile retextures went off without a hitch, not a single issue in-game, in fact, it looks amazing. (ill include an image at the bottom)
I did the exact same process for every texture, so I'm really confused. I was thinking maybe it's because the eye texture file has black empty space between the textures. Could this be something that causes issues?(I'll also include images for the textures at the bottom)

 

[Airist]

Alrighty, I figured it out. For anyone in the future having this issue. It actually had nothing to do with me, the process, or my textures. It was just Citra being stupid. I deleted everything in my extra data folder:

E:\AppData\Roaming\Citra\sdmc\Nintendo 3DS\00000000000000000000000000000000\00000000000000000000000000000000\extdata\00000000\000011C5

edit: this only fixes the after-effects of whatever is going on. So basically the problem persists even on the vanilla textures if you go back, they only go back to normal when you do this. This STILL DOES NOT fix the issue when I reapply the new textures.