Moving some Inbox Emails to subfolders leaves a duplicate copy in the inbox

Hi All hope you can offer some advice on this strange issue we are having.
We have recently installed a SBS2011 server. During installation I updated Exchange to SP3 (which we always do)
We created .PST for each user and imported email using powershell - all Imported across successfully.
The one user have 4gb of email which is made up of inbox and subfolders.
The issue we are having is this  - 
When this user attempts to move an email by either Drag n Drop or Rt Click and MOVE to folder - the email appears in the moved folder but also stays in the Inbox (in effect creating a duplicate)
Now - If I then move the one that appears in the sub folder to another folder - it moves without leaving a duplicate in the original subfolder ......... the one in the inbox is still there though.
I tried logging off and back in - the email is still in both places.
I deleted the one in the sub folder and the one in the inbox disappears as well ??
I have tried it in OWA and Outlook 2013 and the problem still occurs.
I have tried sending a 3mb email into the admin account and re-creating the issue -- but this seems to work fine...
So in summary - its only happening on some emails for some users ...
Can anyone suggest a starting point for this.... I know its real strange behaviour for email and something i have never come across before
Kind Regards
Stuart 

Hi -
This is what I have tried as advised.
1. Created a new .PST file of a users account using outlook 2013
2. Tested that all files move ok when opening the .pst ---- YES they do
3. Deleted emails from users Exchange account using powershell
4. Opened Outlook and confirmed all emails were gone - YES all empty.
5. Re-Imported from local .PST file using outlook on the PC to Import into mail account.
6. Once all folders are updated - tested the emails that were causing problems moving - Problem still the same.
I have checked Exchange and can confirm that this is Exchange 2010 SP3 with Rollup 7 (so culdnt get any more up to date)
Can anyone else please offer any advice / Tips?
Remember this only happens on some emails in the inbox ....some emails move just fine.
The ones that seem to create a duplicate - if I delete from either the inbox or the folder then both go ...so its almost as if its a ghost copy being created......i'm flummoxed though for sure..
Regards
Stuart
Stuart Smith

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