I am having this problem- after enabling security for GIS services, i can't view my maps created for android, in mobile content. I used windows domain users. I can connect to GIS connection, i also can see my published maps, but opening it gives me an error: "The map failed to load.". After enabling security i also couldn't see my published services in web map, error about the tokens. Then i found some information about that. Setting ArcGISApplicationsAppPool Identity to "NetworkService", and setting all applications (KML, Manager, Mobile etc.) to use this application pool, got my web page going, requesting login, and after successful login i see my data.
So i was wondering, maybe my mobile map has something to do with IIS configuration also, because login is successful. I converted mobile folder in "Default web site" to application, and set same application pool, but seems its not enough.