[Petya V4sechkin]

Думал с помощью шаблона setupsecurity.inf вернуть разрешения на реестр и файловую систему

Что-то путаете, в XP шаблон другой %windir%\repair\secsetup.inf
А начиная с Vista это %windir%\inf\defltbase.inf

Иногда его используют, однако по статье KB313222 не рекомендуется:

The use of “secedit /configure” to import the default security template, dfltbase.inf, is unsupported nor is it a viable method to restore default security permissions on Windows Vista, Windows 7, Windows Server 2008 and Windows Server 2008 R2 computers. Beginning with Windows Vista, the method to apply the security during operating system setup changed. Specifically, security settings consisted of settings defined in deftbase.inf augmented by settings applied by the operating installation process and server role installation. Because there is no supported process to replay the permissions made by the operating system setup, the use of the “secedit /configure /cfg %windir%\inf\defltbase.inf /db defltbase.sdb /verbose” command line is no longer capable of resetting all security defaults and may even result in the operating system becoming unstable.

Вместо этого стандартный вариант
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