Visual Studio is designed to take the app.config file from the project root directory and to rename and copy it to the output directory on build. This is by design so that the developer manages the app.config file but can be assured that a proper config file is always availalbe in the build output directory whether it be the debug or release directory
So either manage your applications configuration via the app.config file or remove the app.config file from your project and manage the application config file yourself