Custom textures disappearing

[Darkfire]

So I have this problem:
Whenever I leave the level editor, all custom textures and skyboxes are gone when I re-open it. It also affects the in-game effect. Also, the planes I use are still there, but the material form is blank.
The textures and skyboxes I use are either in /redist/custom_stories/(my story name) or in a subfolder (called "textures", if that changes anything) in the same folder.
I thought you don't need to place stuff in original directories, because when you install a CS it's usually not needed ?
Anyone had this problem ? Or solved it ;p ?