@syncromesh, OK, I'm doing some more testing both with test builds and standalone builds. This first image shows the buildings I chose. Images are numbered from left to right.
Image 2 is standalone of the level that shows only one building with texture the other two buildings are not visible. I will explain later.
Image 3 is the test map run that shows the two buildings that are missing.
Image 4 is standalone of the level that shows three building with texture
Image 5 is the test map run that shows the missing building from image 4.
You should note that the standalone has whole missing objects. I did not have any buildings with transparent walls of the building.
The standalone images #7 and #8 show the contents of the created game. You will note that the highlighted buildings of image #7 do not have any textures copied over. Image #8 has a highlighted path so it doesn't even have the "dbo" nor the fpe of the building. So that's why the buildings are not present.
I am going to add some decals like SHAHIN3D had done to see if it can be duplicated. I am currently using one of the decals from that same pack in a map and I am not experiencing any transparencies. I can't duplicate the decals causing transparency problems.
Alienware Aurora R7 with SSD 256GB boot drive ( C: ) and a secondary drive ( D: ) that is 2TB
Intel(R) Core(TM) i7-8700 CPU @ 3.20GHz 3.19 with Intel Turbo-burst
Installed RAM 16.0 GB
64-bit operating system, x64-based processor
Windows 10 Home
NVIDIA GeForce GTX 1070 with 8192 MB GDDR5 and 8095 MB shared system memory