Hi there, I had your same problem and I think I solved it (in fact I created an account just to help you out!). Basically, I read somewhere (as @The antipodean mentioned) that texture paths are hard coded. Basically, what this involves is (in my opinion) that MO doesn't see any virtual folder that is actually not there in the game folder. For example, I had no modded textures until I manually created the folder "textures" inside my Skyrim/Data folder. I left that folder empty because MO then works as intended. I'm also trying to make that work with sounds (Immersive sounds - compendium for example uses custom wpn_is folder for weapon sounds and coincidentally I'm missing weapon sounds) but since Sounds have an IMMENSE amount of sub folders I'm not sure it's worth the effort. I'm testing how deep I have to recreate the virtual directories to actually make MO load the files as intended. TL;DR // you need to create the folders of your mod path inside the real Skyrim/Data folder, otherwise MO won't load the files. You can leave those folders empty.