Some of the original maps for Swat 3 were made in 3D Studio Max instead of a Worldcraft. These maps will often make use of transparent .BMP files (in Worldcraft we can only use .TGA files for transparency).
There is a way to hack the transparency of the .BMP files. As reported by Alien Abducter:
There is an alpha property for a surface. An unsigned 16 bit number whose range is usually 1 to 255. It's located 42 bytes into the surface (42 bytes after the texture name begins).
As I understand it, if this value is set to zero it should be fully transparent, and if set to 255 fully opaque. Most times it's set to (FF 00) = 255 but sometimes it shows up as (01 00) = 1, which is not quite zero but close enough.
I think that's how they make the living room windows transparent in missiona. In fact if you use scnedit, select those windows, and press z, you can see that in the information for that surface, the alpha shows up as 80h, which is hexadecimal for 50. That's why the windows are transparent even though a_dirtyglass is a bmp file.
I did a test to fix the transparent doors in MissionD (Brentwood). They use a texture called d_dirty_glass.bmp in some of the door frames. The glass was usually set to 0A 00 (decimal 10) in the .SCN file but this is far too transparent. I changed it to 32 00 (decimal 50) and this was a much more reasonable number.