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When ArcGIS Server is installed, a local group is created on the machine called AGSADMIN, which contains users that are allowed to administer the ArcGIS Server.
There is a known issue when a domain group is added to the local AGSADMIN group. Those users in the domain group are not able to administer the server.
An error, similar to the following, is shown when logging in to the ArcGIS Server Manager:
"You must enter an account that belongs to the ArcGIS Server Administrators Group (AGSADMIN) and has administrator privileges on the server machine."
Add individual accounts to the AGSADMIN group.