It is an internal development server so you won't be able to see the links (sorry, I should have removed the link from the address). ArcGIS Server 10.1 doesn't use IIS. It uses Apache Geronimo (Tomcat) as the web server. So my confusion was that by default the Flex Viewer "web server base folder" was pointing to the IIS directory, while the "Web server base folder URL" was pointing to the Geronimo web server (the same as my rest services). I updated the URL to point to the IIS website and now it works.