custom_story_settings.cfg is only used upon starting the custom story. Having several of them has no use at all. If you want the game to find your maps, make a subfolder "maps" in your custom story folder. Move all the maps there. In your custom story folder, there should also be the custom_story_settings.cfg, with the line
MapsFolder = "maps/map1.map"
as well as the other necessary info.
If you don't understand my confusing ramble, read this with thought:
http://wiki.frictionalgames.com/hpl2/amn...stom_story