I have noticed that the ICACLS tool will sometimes set all the require "special" permissions for a basic right, but won't check the "basic" permissions boxes. For example, I granted modify rights to a user, and when viewing the basic permissions window, only Special Permissions is checked. If I drill in to the advanced permission dialogue for the file, and then edit the rights granted to that user, I see all the special permissions required for modify are applied...and I can verify the user has modify rights...so why isn't "modify" checked in the basic permission dialogue?