Windows Server 2008 R2 SP1 using WSUS does not apply patch

server based on Windows Server 2008 R2 Service pack 1 (x64) with installed .NET Framework 4.0 does not apply patch KB2416472 which is approved in WSUS.

Looking at the report in WSUS for this server I see the following entry for this patch:

Security Update for Microsoft .NET Framework 4 on Windows XP, Windows Server 2003, Windows Vista, Windows 7, Windows Server 2008, Windows Server 2008 R2 for x64-based Systems (KB2416472)

Security Updates

Install

Not Applicable

I believe the Not Applicable is the problem - it might have to do with that line saying nothing about SP1. However MS10-070 states that the patch is applicable also for Windows Server 2008 R2 for x64-based Systems Service Pack 1

I've checked the windowsupdate.log file on the machine and there are no references to KB2416472.

Update 1: WSUS version 3.2.7600.226

Update 2: Patch installs manually without problems.

Any ideas?

That update was superseded by KB2656351. Superseded updates are marked as "Not Applicable" if they were not installed before the superseding update was introduced into the environment, since that update contains this fix in addition to new ones..

When looking at the update itself, the WSUS console should tell you that it is superseded and what the superseding update is. I don't have a WSUS server in front of me, so this random screenshot from google images will have to suffice :)