I recently had an error on a new IIS server where it would always return an error for .aspx files. Other files would work just fine. If I changed the version of .net that the site ran in the IIS settings down to v1 it would find the file, just error out because the code wasn't designed for it.
I finally solved the problem by re-installing v2 of the .net run-time. It seems the install got corrupted.