Be sure you have all of these options with correct values in custom_story_settings.cfg:
<Main
Name = "My Custom Story Name"
Author = "The Guy Who Made This"
MapsFolder = "MapDirectory/"
StartMap = "StartMap.map"
StartPos = "PlayerStartArea_1"
/>
You should be sure to change everything in quotes (especially the last 3) to match your situation. Be sure your .hps file has the same name as the map it goes with (ie. StartMap.map goes with StartMap.hps). Make sure you have set a Player Start Area (special area type in the editor), and it is the same name that is in this file. Also, make sure you don't have missing quotes or other symbols that you see here.
custom_story_settings.cfg should be located in your custom story folder's root.