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It would depend on:
- how does windows update determine a patch is installed?
- how does shavlik (bsa) determine the patch is installed ?
There should be some KAs on this in the kb.
Different detection methods are used any and different patch types are tested by default.
Server Automation employs Shavlik for patch detection.
Please see the Shavlik post here:
Why Shavlik Protect Patch Scan results differ from Windows Update
Bottom line is that if you believe that there is a problem, we need to investigate the individual patch.
bsa uses shavlik to perform patch analysis.