A ferramenta Sysinternals AccessEnum pode ajudar. É uma GUI que examinará recursivamente as permissões do local selecionado e permitirá que você veja onde as coisas divergem (se houver).
Do link:
While the flexible security model employed by Windows NT-based systems allows full control over security and file permissions, managing permissions so that users have appropriate access to files, directories and Registry keys can be difficult. There's no built-in way to quickly view user accesses to a tree of directories or keys. AccessEnum gives you a full view of your file system and Registry security settings in seconds, making it the ideal tool for helping you for security holes and lock down permissions where necessary.