This is given due to a manual copy-paste of Config, instead of using symbolic links creation.When I tried to create the symbolic link before, it wouldn't let me and said "a non-empty config-directory already exists."
Solution:
Go into Modules/Server folder and delete from there the manually copied Config folder.
Then go into D3D9 window and create the Symbolic Links.
You should get this:

Your Modules/Server should look like this (note the "shortcut"symbol on the Config folder):

Give it a try.