I had a similar problem with the same building. You need to have all objects separated.
I made the windows transparent, but they were grouped with the building, which also became transparent, so as you did, I separated them into individual objects, but the building was still transparent. It stayed transparent until I broke it down into individual objects.
I use 3ds Max for modeling and export the 3ds.
With "Editable Mesh" you can use the "Explode" function to break up the mesh.
With "Editable Poly" you can use the "Break" function at sub-object vertex level, select all the Verts and hit break
Import the 3ds into Builder and un-group all the parts in the 3ds.
If you use 3ds max , Neil Blevins has a cool Object Detacher Script that does the same thing.
I think this is what you meant
f1virtualr@m