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From The Configuration Manager Support Team Blog:
When attempting to deploy Windows Server 2008 x64 SP2 (KB948465) as a Software Update via System Center Configuration Manager, the update may not be offered as applicable to some Windows Server 2008 64-bit machines.
When you are running an x64-based version of Windows Vista or of Windows Server 2008 on a computer that has multiple Intel x64 processors of a certain kind, or has an Intel x64 multi-core processor, certain known issues were encountered when applying SP2 so detection logic was added that blocks Service Pack 2 on these machines.
For computers that meet this description, you need to have update KB973879 installed. This detail is noted in the following Knowledge Base article:
KB948343 - Windows Vista and Windows Server 2008 service packs are not available for installation through Windows Update
"Computers that have certain multiple processors need to have update 973879 installed for Service Pack 2 for Windows Vista and for Windows Server 2008 to be offered
Some processors report support for some unsupported feature sets. Therefore, when the system uses these feature sets, a Stop error occurs. If this issue exists, Windows Vista and Windows Server 2008 service pack will not be offered for download. For more information and to install this update, click the following article number to view the article in the Microsoft Knowledge Base:
973879 (http://support.microsoft.com/kb/973879/ ) You receive a "Stop 0x0000003E" error message when you try to install Windows Vista Service Pack 2 or Windows Server 2008 Service Pack 2 on a computer that has certain multiple processors "
Some users have noticed an additional issue when attempting to install KB973879. In these cases, the installation fails with, “The update does not apply to your system.”
This can occur if Microsoft Security Update KB971486 is already installed on the same machine. We are working to release a new version of KB973879 with updated detection logic to allow it to be installable when KB971486 is installed but in the interim we have the following workaround:
1. Remove KB971486
2. Install KB973879
3. Configure a Software Update deployment for the client.
4. After SP2 installs, re-install KB971486.
Note: A special thanks to Mike Johnson for documenting this issue.
Hope this helps,
J.C. Hornbeck | System Center Knowledge Engineer
Read the complete post at http://wmug.co.uk/blogs/cliffs_blog/archive/2010/03/04/configmgr-when-deploying-windows-server-2008-sp2-64-bit-as-a-software-update-via-configuration-manager-2007-the-update-is-not.aspx