I've gotten this error when I accidentally allow more than one web.config file in the application's directory or any subdirectory thereof.
For example, I have a folder called Backups in every web app I develop, and I periodically zip up the files in my application and store the zips in that folder. This is fine, until I want to use or view one of the files in a zipped backup. Then I unzip the file and do whatever I need to do. However, if I forget to delete the unzipped files, Visual Studio thinks they're part of the application now, and all of a sudden I have 2 web.configs. The exact error I get is the one you listed.
Hope that helps.