In Visual studio, Solution->Web.Project->Properties->Web, I have changed my Project Url from http://localhost:51123/
to http://localhost:51123/NewProj
If you create an IIS website with the physical path the same as the project folder, and then use it create a virtual folder for the project, you are going to see this issue.
Your Web.config
file is being loaded twice.
Instead as orjanto pointed out, create an empty folder and point the IIS website to it and then use it to create a virtual folder from Visual Studio.