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I don't see where it tells me to fix it manually or how
Yeah really nothing interesting in there...
But if you have no any computer restart during install problematical hotfixes there is way to diagnose trouble with permissions:
1.Download
Process Monitor place it anywhere and run it.
2.Try to install problematical hotfix - if course you have no chance to do it now but it is not concern at the moment -It going on to allow Process Monitor to see where you exactly have trouble,when Windows Update return error save log in Process Monitor (the best as a *.PML file) and then set filter in Process Monitor:RESULT IS ACCESS DENIED
This log show you where you have trouble with permissions but remember probaby only a few of them are really trouble with permissions; remains have only false alarm.If fix all really permissions errors -false alarms disappear either (dominoes effect)