This is happening to me as well, but with clothing/armor mods. making the body parts the clothes wear invisible. Mods that don't use new textures are working fine. Some things I've tried (that OP might want to): Reinstalling the mods, checking that the Texture and Meshes files were downloaded, replacing them with manually downloaded versions, confirming that mods are allowed (sounds like OP's are), testing with similar mods to see if it was specific to those mods, and a few other things I've forgotten (it's been a long day). Right now I'm reinstalling the game, as most manual-mod-install-instructions are referring to differently named files ("Fallout4.ini" while I only have "Fallout4_Default.ini" example). But since OP opened up with a new install I'm thinking that won't work either.