Well, at least thanks to 5shade for trying to help. I found out why it wasn't scaling them correctly.
This is in my case: My computer had a virus resently and that infected every executable in my system. Needless to say, I had to reinstall everything. When I reinstalled Jedi Outcast, I installed it in its default path of D:\Program Files\LucasArts... etc. (D: is my other hard drive). But my old Jedi Outcast directory is still there, known as D:\More Games\Lucasarts... etc. For some reason, when I reinstalled Gtk Radiant, it was using the old Jedi Outcast directory. I changed it to the new one. Yet, it still uses the old one when compiling. Somehow, the compiler has its own sets of tags and information, and right now those tags are telling the compiler to look in the old folder for the new textures, but they're all in my new one! That's when I was getting the error from the compilor, "WARNING: Couldn't find image for shader blah blah blah" and I was looking in my base folder and I actually yelled out loud, "THERE ARE THE IMAGES FOR YOUR STUPID SHADER!! THEEEERRE!!!"
I have not found the correct solution to this problem, but I have solved it temporarily by copying the new textures directory to my old gamedata\base path. It works fine now, since the compiler needs the old path but the game just feeds off the PK3s, I can release this map no problem.
What I may suggest to you, InSaNe1, is to check if your textures are correctly stored in the texture directory in the gamedata\base folder. If they are, and if the map editor shows them correctly, and if you've had to reinstall Jedi Outcast recently or have in the past, check the compiler window when it starts. Note the "VFS Init:" path. If it's not the same as your current Jedi Outcast path, then you need, temporarily, to move your new textures back to the old Jedi Outcast gamedata\base folder. I'm currently working on a way to just plain fix this and have the compiler look in the correct path, but for now, this is the solution.
Thanks for you concern and help, 5hade!! It did help solve another one of my custom texture problems.