Alright, but it only has the black when the plugin is installed.

If you are saying Bleakfalls also has black areas its not your mod causing it.
Take some screen shots of the example to compare the Creation kit and what you see in game.

Multiple parts are. I was in Bleakfalls Barrow and the cave i was in had major black areas. Then i coc'ed to the dungeon I made, and it didnt have floor problems, just wall problems. And the dungeon I made was with dungeone kit pieces.

what objects are you using that are black, are they native in skyrim or part of another mod?

Well I'll try that but it also causes that on the walls. It doesn't affect the ceiling. Mostly the floors and walls.

I would check lighting first, what you seen in the Creation Kit is normally brighter then in game. i have only see black texture on the ground, during world creation. too many land textures in one location cause black spots on the ground. during land edit i do belive ctrl+i will let you see what textures are used in the quadrant. try changing some that are very low % to a more common texture.
Objects that are black are hard to explain unless they are attempting to use custom textures and cant find them.