Wait, so the invisible textures can be fixed by manually installing them? It's not a mod issue, but a problem with NMM?
EDIT: Yep, I checked the Fallout 4/Data folder, and sure enough, the textures folder has all the subfolders, but no files. Apparently meshes didn't install, either. So I'm manually installing these and seeing if it works.
Yea, at least for me. Either manual install or reinstall NMM and Fallout 4 into the same drive. I am not sure which worked but those were the only two things I tried that gave any results. The big hint is if you use a lot of texture mods and if you are never asked to overwrite anything then its not doing something right.