Ok I solved my problem, I was using mod organizer to launch the game straight from the .exe not the launcher...all was well until as I said very recently. But for some reason doing this causes the game to not load from the "Textures" folder and just loads default textures and every other mod folder. Reinstalled nexus mod manager, not in "Program files" because for some reason windows 7 is finicky about that and played through the launcher. It's now loading all the modded folders correctly. A really specific and weird problem solved.