File store migration. 1 old server to 1 new server. 2 folders into 1 ( eventual plan )

I'm currently trying to migrate our File store from our old server running Windows 2003 Server SE SP1, across to our new Windows 2008 Server Standard.  

Our old server currently stores all of our users My Documents folders, which have been re-directed through an Active Directory Group Policy.  We have 2 areas on the server where documents are located...

D:\Data\Users
E:\Data\Users

There are currently 354 user directories within the first area.  14 of these have strangely lost the correct naming convention and now appear as 'Documents' instead of the users name.  If you rename one to what it should be, the rest change.
Approximately 100 appear with the correct name, although their icons have changed from the standard yellow folder symbol, to one with what looks to be an A4 sheet popping out of the top.  

The permissions of all the folders appear fine.  I've tried to transfer the folders across using Backup Exec 2010 ( Backup / Restore with redirection ).  This appeared to be fine at first, however we have noticed that the 114 or so folders mentioned above with either a dodgy name or icon, now appear on the new server as 'My Documents'.  

The folders permissions appear to be fine.  

Any ideas on what is causing this?  Hopefully my attachment 'documents.jpg' makes it a little clearer to see.  ( screen shot taken before copy ).

The second area has a very different problem.  This is to do with permissions.  As Administrator I cannot get access, so using xcopy to transfer changes / updates will fail.  This issue isn't as critical as the first, worst case scenario is I have to take ownership of the 250 accounts manually.

We would really like to merge these folders into one on the new server as it makes for easier administration.  We'll then just have 1 'My Documents redirection policy'.
Documents.jpg
stmonicaAsked:
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David Johnson, CD, MVPConnect With a Mentor OwnerCommented:
There are currently 354 user directories within the first area.  14 of these have strangely lost the correct naming convention and now appear as 'Documents' instead of the users name

for admins deny read to "desktop.ini" and the folder names will reappear.
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Lionel MMConnect With a Mentor Small Business IT ConsultantCommented:
This is a quirk in Windows 2008 (and Vista, Win7, 8) as well as Server 2012. It sees that it is a Document folder (the Old My Documents folder). However if you double click on it and then look in the address you will see that its says documents but if you then click on the address it will show the real folder names. The way dealt with it was to have a folder structure like this
E:\Data\Users\%UserNames%\ so there will be folder created for each user's name and then their documents will show up under that. Example E:\Data\Users\Bob\Documents
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