Btw. For GtkRadiant you'll need a second install of q3 to make maps in...
Edited 12.39 hours after the original posting.
Create a new directory and call it something like "quake 3 clean". In that folder, create a "baseq3" directory.
In the baseq3 folder, place a copy of all the "pak*.pk3" files and nothing else. In the "quake 3 clean" directory, place a copy of the main "quake3.exe". Click the "quake3.exe" to start a clean copy of the game. When you are asked for a CD key, just press ESC.
To test your map, place your pk3 in the clean baseq3 and nothing else. Be sure to only keep what you are testing in this clean version.
Some people don't test out their new maps on a clean install but instead, test them out on a used install with other map .pk3 files such as those mentioned above residing within the base folder and as a result, they don't see the missing textures. However, you also have people who don't even test the maps in a run through which doesn't help the integrity of the publicly releases map.