Hello, I recently did a clean install of skyrim since as I wanted to start over with fewer mods. Since reinstalling, about 50% of all mesh and texture replacements are overridden with vanilla meshes and textures. I have reinstalled several more times, and the issue is still present. The game still uses some of the mods, but not others. An example being that it will overide better females by bella, but the same files from coverwomen are not being overridden. I tried to find a solution to this, but the closest I could find to this issue was the high res texture pack overiding custom textures, and that was ruled out after I deleted it. I am starting to wish I had never tried to start over.

See here: http://www.gamesas.com/topic/1354395-update-bsas-and-you/

Thank you for that, but there isn't really anything in that thread that I can link with my problem, interestingly enough, it still overides my textures when there is no BSA for it to overide them with. In a failed attempt to fix the issue, I unpacked the texture.BSA file into the data directory, moved the BSA into a backup folder, and then replaced the textures I wanted, and it still is using the non existant default textures. I can't figure out how it can use textures that no longer exist.