This has happened to us before and now we have the steps to hurriedly changed the permission settings back to what they need to be, but this is kind of a pain in the butt. What usually happens is if we do any changes to our VM where our ArcGIS Server sits, we lose all of our permissions and it sets back to, what I'm assuming is default token authentication?
We use windows authentication to access our web services for our apps, and after a reboot of the server, the services all lock up and nothing can access them. There's a lock symbol next to all the services in ArcGIS Server Manager (even for me with admin rights) and my apps ask for usernames and passwords. The steps I take now (thanks to ESRI Tech support) is to go into ArcGIS Admin Directory, go to the services, then permissions and type in esriEveryone in the Allowed Principles- or do a clean and re-add it in.
Those steps fix the problem and our services are back up and running and no permission issues- yay. But, what I would like to know is why it does that and is there anyway we can fix it so when we do any reboots or changes to our server that we don't lose our permissions. We use ArcGIS 10.2