Why would Folders be read only on a file server?

Im running into a weird issue I hope you all can help me with.

I have a Dell PowerEdge 2800 running Windows 2003 Enterprise. It has 10 physical drives - 2 of them mirrored for the OS and the other 8 running RAID5 with 2.1TB of storage.

Programs I have installed
- Wincloak by ScriptLogic
- Diskeeper 10 Standard
- SAV Corporate
- Server SP1 and all Windows updates

So nothing out of the ordinary. However, about 2/3rds of my directories on the server somehow moved to read only. When I remove the read only, force it to remove the read only to all files/folders under the root, it removes it fine. I close say the My Computer applet, when i open the applet again, browse to a folder/drive, the read only is back in place. I have called Scriptlogic to see if WinCloak could be causing this, they explicitly deny no its not. I dont know what else could be causing this. Any help would be greatly appreicated.
dsheltzelAsked:
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Pete LongTechnical ConsultantCommented:
All Folders Are Read only?

The square (or greyed out check mark) for a folder means NOTHING, NO CHANGE, WAITING
FOR YOU TO USE ME.  This is because the read-only box in a folder's properties is
only used to apply or remove the read-only setting from all of the folder's files
at once. If you clear the box and click Apply, then the files in the folder will
be cleared of any read-only attributes they have. Like wise for checking the box
to apply the attribute to all files.  The square reappears the next time because,
once again, you haven't used it.

FOLDERS do NOT have a functional read-only attribute in Windows.  The read-only attribute
is only for files.  The read-only check-box for folder properties is a bad and confusing
design.  If you want to avoid read-only confusion, check individual files, ignore
folders.

Windows file systems actually use the read-only attribute for a folder to make it
customisable, but the checkbox in a folder's properties has nothing to do with that.
 You cannot prevent a folder's contents from being changed using the read-only attribute.
 You can read more about that here:    

http://support.microsoft.com/default.aspx?scid=kb;en-us;326549

From http://www.annoyances.org/exec/forum/winxp/1065399208
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Pete LongTechnical ConsultantCommented:
ThanQ
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Windows Server 2003

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