I had a tough time finding a clear answer to where I ought to install based on my system specs even after watching vids from Gopher, GamerPoets, Phoenix, etc., so I took my best shot and I have my installed mods in a folder in the /common folder of Steam on my SSD but my mod download folder and almost all of my modding utilities are on a storage HDD.
OK, so that is part of the problem. I'll try to make this as clear as I can, using my own setup as an example:
STEAM - Should be installed in it's own folder, outside of any UAC protected areas. (C:/Steam, in my case).
SKYRIM - Installed in the normal Steam location.
TOOLS - Away from UAC controls, and NOT in the same folders as Steam. For each tool, a new folder inside that tools folder. (C:/Tools/ModOrganizer2, C:/Tools/xLODGEN, etc).
They should all be on the same drive as well - I've seen a few people try to split things as you have, and I don't think it's gone well for a one of them. It'll take some time, but you need to reorganize your file structure to get it all to play correctly.
[EDIT] Discovered this is caused by coc'ing while on horseback.
I had a moment kind of like this yesterday with ENB acting up... something that is obvious in hindsight, but frustrating as anything when you did it. Chip up - you're almost there...
Then the REAL game starts... updates and more mods, of course. You didn't think I meant Skyrim, did you?