As you already noticed subinacl is not for x64 -I don't know why so many moderators can't accept it as offered fixes are appriopriate for XP not for Vista -making succesfuly on Vista will be permission violations.Fortunately the owner of C:\Windows folder is TrustedInstaller so these reset.bat for XP or likely will never work even on x32 system.
Download Process Monitor Process Monitor
Run Process Monitor,next run Windows Update and try install something.When WU will return save log in Process Monitor in *.PML format,pack this file to .7zip or .RAR and upload on RapidShare: 1-CLICK Web hosting - Easy Filehosting
There is tool for x64 (of course apart build-in icacls which is many time failed) is SetACL SetACL - Windows permission management
-although this tool have trouble with services accounts for example TrustedInstaller...much to describe
But do not use this without my order