I spend weeks trying to find the perfect way to level edit BSP maps and in 5 mins I suddenly solved the lot. Here is my guidance on Quake 3 BSP.
1/ turn fog off/on if you a visual problem but you know the bsp has loaded.
2/ quaRKE will put your file format exactly as it should be in your pak file. What I did was to copy the Q3 Pak file into my game worlds dir(where you want your pak file to be),
open the pakfile with PAKSCAPE and deleted all the prviouse info that was used in the game (thats why I copied it first). Then I copied ALL the files in the tempquarke file (but not by copying tempquarke ) and pasting them into the pak file(again opened with PAKSCAPE). This worked. I do suspect, but have not tried it, that quaRKE will make the folder layout for you. When all your levels are completed paste the lot as quaRKE has done it straight into your empty pak file.
3/ BUT...I here you say, I'm still getting black textures!
I suddenly realised that Q3 uses it's floor textures to identify what sound the footfall should make in different part of the world. A feature not supported by DBPro.
...SOLUTION...Texture the floor with a file from the BLOCK file. It is the first texture file you will find. It is the same for the ceiling. Do this and you may just think Christmas has come early...or again.
I've tried to be clear. If your stuck post extra questions.