I let the game generate new .inis. Nothing.
Edit: I deleted them from docs/skyrim. Where are they in the install folder?
And to delete the mods should I just delete the Data file and let Steam DL a new one? Should I try running through the normal launcher instead of the 4GB launcher (didn't change anything though).
Lol wow I knew you had something on that wasn't stock

Delete and disable anything, and run the game at stock settings as though it's a fresh install.
Where steam is installed, steamapps/skyrim.
This will fix the problem. Promise.
Afterwards, add your bits and bobs one by one, see which caused the problem.