I use Web Deployment Projects to build an ASP.NET web site.  

When I built the web project by itself I got a successful build, but the Web Deployment Project received the following error...

The virtual path '/UserControls/Common/ModalProgress.ascx' maps to another application, which is not allowed.

I scratched my head for a few minutes then decided to try adding the ASP.NET root operator "~" in front of the path name.  So, the path became '~/UserControls/Common/ModalProgress.ascx'

After making this change I was able to build my Web Deployment Project.

For more info: Web Deployment Projects and ASP.NET Paths