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KB269308 does not have a publicly available link and therefore is not supported by Protect.
If the file version ntkrnlpa.exe is less than the expected version then Protect detection logic is working correctly.
I suggest ensuring you are running the default built in WUscan without patch groups or custom actions.
WUscan shows the same patches as needed.
I see that the download link requires validation and I understand why you can't support that. But, you're comparing LDR and GDR version numbers and generating a false positive.
I have the same problem with Windows 2008 R2 Standard (x64) SP1. Windows update installed KB2639308 overnight. The next morning, Protect thinks MSWU-514 and MS11-068 are missing.
Looks like your latest XML fixes this. Thanks.