I've seen it but can't remember resolution.
From the Help:
If you encounter a failure when creating or joining an ArcGIS Server site, you can troubleshoot the issue by addressing the error messages reported in the create site or join site summary panel. Additionally, a log of the event is recorded on disk, located at <ArcGIS for Server installation directory>\ArcGIS\Server\usr\logs\<machine name>\server. The messages in the log can provide additional insight into what caused the issue. To view the log, navigate to the logs directory and open the log in a text editor.
Maybe the logs will give a clue