I'm having sort of the same issue, but where my mods are working, my textures, across the board, are not loading at all. Example: I'm using The Rebel clothing set, and when I put it on, I basically just turn invisible.
Happened to me a few days ago, 4 times in a row in less then an hour. f*#@ing bethesda. Decided to blow it all out, and reinstall everything and now I can't even get the damn game to run.