I am using GTKRadiant 1.3 for JA and non of my shaders work... Even in the sample lvls the shaders are screwed up.. they all say "shader not found".

It's a re-install GTK thing! 1.3.12

Try removing any downloaded map files. I know that alot of people who made levels for jedi outcast made them "compatable" with jedi academy by just copying the images+folders from jo, and pasting them in a textures\jomap folder with their map. Whenever you load the specified map textures, you will also get theirs, and they ussually don't insert the shaders.

I had the same problem, then i just deleted the matrix map, and all others that had people too lazy to change the image directory. The false images disappeared along with the shader warning.

This might help, but you might also have a different problem.