So I wanted to make a quick post regarding MVC with new applications (Internet or empty) that got me a few times now, so I can only imagine how many others this has nailed.
Apparently there is a "Known issue" where some MVC applications are not able to get the User.Identity populated with just authentication ="Windows".The known issue was found under Known MVC issues
In some cases you are also required to add the following line to the <appSettings> section of the web.config:
<add key="autoFormsAuthentication" value="false" />
Hope this helps some folks in their MVC journey!
Dan Lewis’ Development and Technology Blog