A you can see by the images, any object I that intersects or contracts an object with the above texture holes begin to appear inline with the object. The above example has has a subtractive box with another box with the windows texture. I’ve used multiple objects and they all cause the same problem. The texture I’m using is form gametextures.com and other textures I have from them work fine. I have made sure the material is mapped correctly using the gametextures.com tutorial. Anybody have any clue what is going on?
In this case it has nothing to do with the textures.
It is probably the bsp you used.
Bsp is not designed for this kind of work and complex/overlapping pieces of bsp can give strange errors.
Back in the day we would call them bsp holes (created by the UEDGoblin).
(This is because the bsp needs to try and make its own polygon cuts, and not always can do a good job at it depending on the complexity of the bsp cuts)
Either try to convert the building into a static mesh, or use the sensible way and create the mesh from scratch in blender, maya, max or any other 3d tool of choice.