Okay, that explains everything. You missed out or misunderstood crucial steps of my tutorial.
Try this for your
main_init.cfg file:
<ConfigFiles
Resources = "Medusas Den/md_config/resources.cfg"
Materials = "materials.cfg"
Game = "Medusas Den/md_config/game.cfg"
Menu = "Medusas Den/md_config/menu.cfg"
PreMenu = "Medusas Den/md_config/pre_menu.cfg"
Demo = "config/demo.cfg"
DefaultMainSettings = "config/default_main_settings.cfg"
DefaultMainSettingsLow = "launcher/default_main_settings_low.cfg"
DefaultMainSettingsMedium = "launcher/default_main_settings_medium.cfg"
DefaultMainSettingsHigh = "launcher/default_main_settings_high.cfg"
DefaultUserSettings = "config/default_user_settings.cfg"
DefaultUserKeys = "config/default_user_keys.cfg"
DefaultBaseLanguage = "base_english.lang"
DefaultGameLanguage = "english.lang"
/>
<Directories
MainSaveFolder = "Medusas_Den"
BaseLanguageFolder = "Medusas Den/md_config/"
GameLanguageFolder = "Medusas Den/md_config/lang/"
CustomStoryPath = "custom_stories"
/>
<Variables
GameName = "Medusas Den - An Amnesia: The Dark Descent Mod"
/>
<StartMap
File = "00_intro.map"
Folder = "Medusas Den/maps/"
Pos = "PlayerStartArea_1"
/>