For some reason the Make VS.NET cannot load a web project that is located under nested virtual directories.
Example
http://localhost/virdir1/virdir2/webproject.vbproj
If virdir2 would be a physical directory under virdir1, the project loads fine.
To workaround the problem I am calling devenv.exe directly. This works fine, but its definitely not ideal as I have to write the rest of the functionality provided by Make VS.NET myself.
I am using Visual Build Professional 6.1