First some background. At the end of 2012 we migrated our vs2008 solution to vs2010 but we still target .NET 3.5. (I know nothing but the latest and greatest here!)
A simple solution to this problem:
Go to the following path:
C:\Program Files (x86)\MSBuild\Microsoft\VisualStudio
You will see the latest version V10.0, v11.0, v12.0 depending on your Visual Studio 2010, 2012 or 2013 install.
Copy WebApplications folder from either of latest version directory and paste to other.
Your issues should be resolved.