So I had a good Skyrim going. I was using Mod Organizer and installed many mods. Everything was peachy. Then I entered Breezehome in whiterun and then the bannered mare. Both buildings' interiors had little slits in the ceiling that allowed me to see out into the sky-like abyss. I know for certain it is not a part of the normal Skyrim game.

Long story short, I ended up disabling ALL of my mods to try to see which mod might be the culprit of the error, the bad mesh/texture persisted. I loaded from Steam, got the same thing. I checked file integerity, it still persisted. Then I removed skyrim from add/remove programs, did a search for skyrim on my entire filesystem and deleted all Skyrim stuff(basically just the skyrim folder in the steam folder and the games folder with my saves and .ini's) except for the skyrim mods downloaded in MO. I then redownloaded skyrim and ran it with out ANY modification done to skyrim whatsoever. I STILL get the same Transparent slits that let me see outside of breezehome and the bannered mare.

Totally clueless at this point. What can linger even after a total deletion and reinstall?