No, my files are in the right spot. The textures all show up fine in radiant....well, the majority of them do.
Most of the non-texture shaders won't show up in radiant, but show up as black and blue checkerboards. Shaders such as Clip, Area Portal, NoDraw, Kill, etc.
It isn't a huge problem. I can make the map without seeing their textures (obviously), but when I compile it does still give me warning that the shaders aren't found for them (howerver the map still runs fine, obviously).
I just find it a pain in the butt not being able to quickly tell what the brush is by looking at it. Pink = caulk, etc. It's hard to keep organized when your caulks, nodraws, fogs, and area portals all look the same.
Having the bright pink caulk is really helpful for looking for leaks as it stands out. I find myself checking the textures of half my map when I end up with a leak since I can't tell which is a caulk or not.
Hmm, well all those shaders you mentioned are stored in your BaseEF/scripts/common.shader file. If they aren't loading up then Radiant isn't reading that file.
Make sure your Radiant paths are set up right. Make sure the word "common" exists in your scripts/shaderlist.txt file (usually it shows up at the very top)