This occurs only because the sample builds in the TEMP folder, whose value is provided as a short filename, and VS.NET thinks the virtual directory path is different than the project file's path (because it does an [invalid] comparison of a long filename to a short filename) and issues the error message. As long as you avoid performing your builds in the TEMP path (or change your TEMP path to something like c:\Temp) this shouldn't be a problem.
Another option for more robust automated builds of web applications is to avoid VS.NET web projects altogether:
http://www.pluralsight.com/fritz/Sam...b_projects.htm