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Windows 2008r2 NTFS permissions not propogating down to subdirectories

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This is crazy.  I have been working with Windows servers for 15 years and you think you know how they work but then something like this happens and you realize how dumb you are or how screwed up Windows settings can become.

Issue: I am simply trying to change permissions on my directory structure on a Windows 2008r2 server.  For some reason the perms are not propagating down correctly(the way I think they should) to all the sub-directories below.

Environment:

-Dir1
    -Dir2
    -Dir3

When I set perms on Dir1 it should propagate down to Dir2 and 3 if inheritance is set.  But, when I set perms on Dir1 then check the perms on Dir2 and Dir3 they are different perms.  I am simpifying this environment for the purpose of asking this question but this is basically what is going on.  I am using get-acl and set-acl to make the permissions change through a powershell script but that should not matter either.  Can someone help me clear this up or shed some light on it for me?  I feel like a clown.  thanks


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