A patch has been released for an ArcGIS Server 10.1 SP1 issue, which can be downloaded here.
This addresses the following bug:
NIM090171 - Shutting down and restarting the ArcGIS Server Service when using the IIS and Java web adaptors can cause the REST handler on the restarted node to lose all principals, specifically esriEveryone, at the root level forcing users to log in for every request.
In English, this patch addresses an issue where all services become locked or inaccessible in situations where ArcGIS for Server is restarted under load. This makes services unavailable until ArcGIS for Server is restarted again. If problems are encountered with symptoms similar to this it would be worth installing this patch, as it has been found to resolve a number of related issues.