I'm using AGIS Server 10.1 SP1 on Windows 2008R2, SQL as the user store, GIS Server as the Authentication level, and the WebAdaptor unsing IIS.
I have a folder secured and others that are not. The secured folder requires Token authentication for a service used in a javascript app with a long lived token, and using authentication makes the service visible in the REST endpoints. This works fine most of the time. However I have had problems with the Token Service occasionally failing or stopping. This results in the web application failing to authenticate and does not draw the map, but it does not kill the application. When this happens logging into the REST site also fails to authenticate and will not provide access to or even display the secured folder but it appears that the login works.
Is anyone else having problems with the Token Service stopping or failing? My only solution at this time is to either restart the ArcGIS Server using ArcGIS Server Manager, or physically restarting the machine. Recycling the WebAdaptor app pool in IIS does not clear this. Open services (those that are not secured) do not seem to be effected--they remain visible and the apps using them work fine.
Any ideas or shared experiences with this are greatly appreciated!