Windows Server 2012 - data seems missing

This is a wierd one.   Thought I'd throw it out there.   Setup a new 2012 windows server.  setup networking, cname, etc.   Then I went ahead and re-partitioned the Data Partition as a 1.99TB partition, formatted with default NTFS as drive E.  Called it DATAPART1.   Copied 100GB of data over from the old server (preparing for migration later this week).   Then went ahead and joined to domain, upgraded to a domain controller, moved all FMSO roles, etc etc from old windows 2003 domain controller.   All worked like a charm.   All windows updates done etc. yesterday.
Went in a bit ago to setup server backup, DHCP, and share permissions on some of my data folders on the E partition.   They seem gone.  When I look at properties of the E drive, the data is there.  If I try to create a DATA folder on the root (which is where I originally created a folder and put my data in), it says "already exists...want to merge."   Checked to see if the Attributes changed to hidden but when I view hidden doesn't see it.
Very wierd.
Any ideas?    I can always format the partition again and resync the data, but since 2012 is so new, wanted to see if anybody knows what might be going on? Any ideas would be helpful
This isn't a VM either
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Obvious one, but have you enabled show hidden files show OS system files?

If you open the drive in a command prompt and type attrib, is the data listed?

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fitzpabAuthor Commented:
Good obvious question.  Did the show hidden which didn't see, but showing protected OS files saw them.  
Must have been something in the dcpromo that did that.  Strange.  So I am changing attributes now and will update this after my morning meetings.
fitzpabAuthor Commented:
Ended up being my sync software (3rd party tool) which was changing system and hidden file attributes.   Was able to reconfigure and all good now.  Thanks.  Got me on the right track
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Windows Server 2012

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