I am also having this problem.
This is the structure of my folder: Custom Maps > testmap (containing custom_story_settings.cfg) > maps (containing testmap.map and testmap.hps).
The contents of custom_story_settings.cfg are: 
<Main
	Name="The Test Chamber"
	Author="Anonymous"
	ImgFile=""
	StartMap="testmap.map"
	StartPos=""
/>
From my hpl.log I have found what I believe are the relevant errors: 
Game Running
--------------------------------------------------------
 -------- Loading map 'menu_bg.map' ---------
    Cache Loading: 2741 ms
  Entities: 758 ms
  Compilation: 1 ms
  Total: 3557 ms
  Meshes created: 26
  Bodies created: 5
 -------- Loading complete ---------
 Setting profile: 'dev_user' Path: 'C:\Users\Kyle\Documents/Amnesia/Main/dev_user/'
ERROR: Unable to open config file 'maps/main/ch01/custom_story_settings.cfg'! Invalid filepointer returned!
Error creating custom story from path "maps/main/ch01" : could not find custom_story_settings.cfg file or it was invalid.
ERROR: Unable to open config file 'maps/main/ch02/custom_story_settings.cfg'! Invalid filepointer returned!
Error creating custom story from path "maps/main/ch02" : could not find custom_story_settings.cfg file or it was invalid.
ERROR: Unable to open config file 'maps/main/ch03/custom_story_settings.cfg'! Invalid filepointer returned!
Error creating custom story from path "maps/main/ch03" : could not find custom_story_settings.cfg file or it was invalid.
ERROR: Unable to open config file 'maps/main/MyMaps/custom_story_settings.cfg'! Invalid filepointer returned!
Error creating custom story from path "maps/main/MyMaps" : could not find custom_story_settings.cfg file or it was invalid.
I am fairly certain that whatever the problem is, it is my fault. I screwed around with the usersettings.cfg and mainsettings.cfg files in an attempt to follow the instructions from the wiki here: 
http://hpl2.frictionalgames.com/amnesia:devenvguide
I gave up on not being able to find some of the options required to be changed. If you think it might help, I can just reinstall the game and work from there.
Thank you for your time, and I apologize for the long post size.
EDIT: Progress! I repaired the settings files that I mangled, and now the string of errors is considerably smaller. I have updated that section of my post to show the new contents of the hpl.log.