Well.. I have put textures and shaders that didnt appear on Radiant, like my physics_clip comes out as a see-through "Shader not found". The shaders still work though.
I also have made some of my own textures that have errors when I load them, and come out as "Shader not found". I compiled to find out if they still worked in-game. These are usually images, posters for on the walls, and other things of that sort that are thin.
The error is:
WARNING: JPEG library failed to load textures/vos/kurtcobain.jpg because progressive JPEGs not supported, use regular JPEG intead.
WARNING: Activate shader failed for textures/vos/kurcobain.jpg
The image in this example is a poster of kurt cobain... I made a really thin brush and put that texture on there, is that the problem?