The textures you make goes in a pak file, Quark only makes a texture folder in the roarke folder for editor purposes. The game uses only the pak file with the textures inside it, not the texture folder that apears because of Quark done this in the roarke folder.
For new textures :
you see a "cloth" tab in Quark with new textures. "Cloth" folder must be in pak also, that
the texture must work.