Check the Full LOD box in the reference window. This is a known issue. Aparantly, after checking that box and saving, you may even be able to uncheck the box and still have your build fixed, as the LOD is lower quality so while it doesn't load the actual LOD object, it will look a bit worse.
When you say disappearing you mean that the building is no longer visible after you fast travel? Have you clicked on the building in the CK and checked the box "is full lod" ? I placed one of the Orc longhouses and it was invisible in game, so i did the above and it works fine now.