Ok, here is the deal - I made a nice hallway, and my FPS was horrible - unplayable. So I made a backup of the hall, and began to remove things (this is after I tried making some things detail brushes), and tested and retested, and every time, my FPS is shot - the same. I seriously am left with just a rectangular box, and some red lights. I tried making items detail brushes, tried removing just about everything, tried even moving the map around in case it was crossing leaf nodes, and still have the issue - note, this is the beta GTKRadiant (the one GothicX linked to), and I am making a JA map, if this helps any. The map is light on shaders too, so it's not that either.
So, anyone have any ideas?

are you making sure the unseeable textures are caulk?

No, that won't matter.

Turn off dynamic glow, it's buggy until the patch.

r_dynamicGlow 0

Actually, I picked up Release Candidate 3 today, and the Dynamic glow is fixed. all is right in the world, lol...

Erm, what? GtkRadiant doesn't have dynamic glow, nor does it interface with JA at all, and it cannot fix dynamic glow... What are you talking about?

Sometimes when I'm running GTKradiant and test my map in JA the game will just run at 0 FPS. I had the same problem with JK2radiant (in combination with JO), so it seems it's rather a problem with my pc then radiant. Solution, don't run radiant when testing a map :(

Just go to File -> Sleep before running the game.

hmm. Well, all I was saying is that my issues got solved when I used the RC 3 of GTK Radiant and compiled with it, without having to turn off dynamic glow. I really don't have the foggiest on how things work behind the scenes.