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You may find a security assessment report that recommends you change the Access Control List (ACL) for ProtectedRoot certificate store in the registry.
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Microsoft does not recommend making this change to the ACL for ProtectedRoot certification in the registry.�
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Changing ACL�s on certificate stores is not supported or tested. Functional impairment can be the result and careful testing for the customer specific situation/effects is recommended.
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Controlling the root ca list can be done by GPO and there is no need to modify the ACL�s on the persistency containers to achieve the target. Check the documentation on �Enterprise Trusted Root Certificates�
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http://technet.microsoft.com/en-us/library/cc758128.aspx
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