Windows 2012 Server Quota Problem

I am using Windows 2012 Storage Server to serve out Home folders on my network.
I have set quotas on each employee's Home folder.
I have one user's folder (Joe) who shows this strange info:

If I right click on Joe's folder I see --> 563MB used.
If I look at the backup for Joe's folder it shows --> 1.88GB
Joe's quota is at 40GB and it's telling me he's used 100% of his quota!

Can't figure out why the server is telling us he is hitting his quota.
Where is all the other data coming from?

- No other user has this problem.
- If we raise the quota he eventually hits his quota after a few days.
- The volume that contains the Home folders is running Shadow Copies.
- We tried re-creating Joe's Home folder but the problem comes back.
- Joe is using a linux machine with Oracle Virtual Windows (no other users with his configuration are having this problem).

Any clues would be helpful.
Thank you!
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Just a clue due you use shadow copies....
If Joe changes the content very often, the shadow copy gets larger and larger...
Also possible that there are orphaned shadow copies...
Have a look into device manager if there are a lot of disabled shadow copies (with hidden items are shown).
rr4406pakAuthor Commented:
I looked in the Device Manager and then under the hidden Storage Volumes. I found some "Generic Volumes" that were greyed out. It is unclear if I should delete these or not. Some sources say to leave these as they are and not delete them.
Keep in mind I am not having trouble with the server.
It is just one user going over his quota... when he really isn't...
Yes, I understand....
If you see grayed out shadow copies, they might be connected or even not. If you delete them, you may also delete the shadow copy  data itself. As more shadow copy dates you see in the drive properties, as more shadow copies are there in Device Manager....
Nevertheless not all of them maybe active, especially as there was a problem in the past, where orphaned shadow copies staid there and produced performance issues.
See also KB982210

The KB talks about backups and temporarily connected drives, but I have seen it also on server, where never other devices where connected. Some servers had hundreds of shadow copy devices nevertheless shadow copies where switched off.

If you switch off and delete all existing shadow copies (from the drive property dialog), the grayed out shadow copies in the device manager should disappear. The used space should go to zero. If some of them are left over, they are possible orphaned items.  

There is a tool called DevNodeClean.exe from Microsoft.
DevNodeClean.exe /r should remove orphaned items in the Device Manager.
It removes orphaned disc as well as orphaned shadow copies. Other items like USB disc etc. stay even they are not connected.

But no warranty for the tool, I used it several time and could not investigate issues.

If you have another disc, you may move the files to a different drive and share the folder there, just to see, if there is a difference in the behavior.

What else is stored in the "home" folder, only user files or also files from the user profile?
I guess you checked it for hidden and system files, right?
rr4406pakAuthor Commented:
Found what worked in this case is, in the Quota Management area of the File Server Resource manager, totally deleting the quota and recreating it for the folder in question. Seems to be acting normally now. No idea what caused it. Thanks.

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rr4406pakAuthor Commented:
Found the answer myself.
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Windows Server 2012

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