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KB Article: http://support.microsoft.com/kb/977507
INTRODUCTION
When you connect to a remote application by using Remote Desktop Web Access (RD Web Access) on a computer that is running Windows Server 2008 R2, the Connected icon does not appear in the notification area. Note When you first run a remote application, the Connected icon appears in the notification area.WebSSO (Web Single Sign On) does not work as expected, causing a "double prompt" for credentials in applications launched via RemoteApps published via Remote Desktop Web Access in Windows Server 2008 R2.