When you logon to a Windows Server 2008 (R2) server with a Administrator account, Server Manager is started automatically. If you don’t want the server manager to start automatic you can prevent this by setting the following registry key:
Create a new Dword value “DoNotOpenServerManagerAtLogon” in the registry key HKEY_CURRENT_USER – Software – Microsoft – Servermanager and set the value to 1
Next time you logon the Server Manager will not be started at logon. You have to set this key for every user you want to prevent automatic startup, because it is a user setting.