Ad,
I don't beleive you can supress this message from showing up using group policy. You have installed updates on the server, and it needs to be rebooted, which means ALL users must be off of it, and therefore ALL users receive the message.
Having said that, the bigger question is why did you install any updates to the operating system when users were logged in? You potentially could have changed out some underlying OS code that these sessions were making use of.
Best practices for Terminal Server updates are to have all users log off the system, run the updates and then reboot.
Now, if you want to configure the updates to download, but not install automatically, you can certainly do that through group policy. Load the Wuau.adm template, and configure the automatic updates to auto download and notify for install. This notification will only notify logged in administrators, not users or power-users.
Here's a link to the technet article that talks about managing WSUS through Group Policy:
http://technet2.microsoft.com/WindowsServer/en/library/51c8a814-6665-4d50-a0d8-2ae27e69ca7c1033.mspx?mfr=true
Hope that helps
Thanks
Eric


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