Symptoms
The error is "System.DirectoryServices.ActiveDirectory.ActiveDirectoryServerDownException: The server is not operational. Name: "..." ---> "
There are multiple domain controllers.
Diagnoses
We linked it to TFS _543801 and supplied the coldfix
Resolution
Looks like the coldfix didn't resolve the issue.
"The root cause was a config issue with the intranet security option in IE 9. We fixed it with a GPO."
Seems like an update to the Group Policy settings fixed this issue.