Windows Server 2003 and missing disk space

I have an account with a Windows Server 2003 that is running out of disk space yet much of the space in unaccounted for in Windows Explorer making the problem difficult to resolve.

When I right click on the drive icon in My Computer and choose properties I get the following (all of the below numbers are rounded for simplicity):

Total space available on the main hard drive - 434 GB
Total space used - 426 GB
Free space - 7 GB

But if I open up the the drive in Windows Explorer, select all files and folders (yes, I am showing hidden and system files and folders) and choose properties I get:

Size - 131 GB
Size on disk - 131 GB

This is a discrepancy of about 295 GB, which is the majority of the drive.

I ran check disk which showed that my clusters are set to 4096.  The numbers from check disk also showed that 426 GB is used (so check disk agrees with the output from the properties of the drive, not from Windows Explorer)

My suspicion is that somehow permissions have been messed up with many of the files and folders on the drive, so even though I logged on as Administrator Windows Explorer isn't showing me everything.  I've looked at the security tab of of the drive and Administrator is listed as the owner.

Here's my question, there is an option to "Replace owner on subcontainer and objects".  I'm thinking that this may solve my problem, but I am concerned that this may cause other problems.  So, might this solve my problem so Windows Explorer's output is correct?  Could this cause any other problems on this server?
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Run this on the server instead to see if it reports any differences...

Treesize -

Or this one is good

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Thomas GrassiSystems AdministratorCommented:
Has this server crashed in the past? Dump files sometimes can take up a lot of disk space and they are hard to see.

What about paging files check that out also.
Jaroslav LatalMSPCommented:
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Right-Click My Computer>Manage, select Disk Management. See if this can help you decipher where it is all going.

perhaps the Hard drive was partitioned in some way?
dcpwebberAuthor Commented:
Responding to smckeown777:  Treesize shows what check disk shows, 400+ Gigabyte of data and only 7 GB free. It also shows one of the shared folders has 373 GB in it (Windows Explorer shows the same folder to contain only 97 GB)  So, Treesize (and check disk) can see the data but Windows Explorer can't.  Is there some way to fix this?

Responding to trgrassijr55:  Yes the server has crashed in the past, but I would think if I had viewing of hidden and system files and folders turned on the dump files would be accounted for.  Also, the paging file is visible in the root of the drive and so is part of the Windows Explorer data

Responding to JardaCZ:  Shadow copies are turned off (due to lack of disk space)

Responding to TechOps07: The physical drive is partitioned.  One of the partitions is where the space is missing - it's a 400+ GB partition that has about 300 GB unaccounted for in Windows Explorer.
Ok, but Treesize allows you to drill into the folders to see which is the largest - can you do this? Not sure why windows isn't reporting the size correctly - possibly you need to run a chkdsk on the drive to clean any potential issues...
dcpwebberAuthor Commented:
I ran a chkdsk /r over the weekend but the problem persists.

Yes I can drill down, but I'm still confused why Windows Explorer isn't seeing things correctly.  Since it's a shared folder with user data and not a system folder, I'm going to go the take ownership route and replace the owner on the subcontainers and objects, I'll update this item with the results.
The shared folder - does the default Admin not have access to it? Meaning the account that you are viewing the statistics with? Taking ownership is over the top I'd say, well depending on the underlying permissions for the other users...but if its not too much work then ok

Using Treesize is there one folder that appears to be taking a big percentage? I'd check the permissions on that folder first - possibly someone(user) changed something that is blocking windows admin account from seeing it
dcpwebberAuthor Commented:
I went to the shared folder and took ownership, I specified "replace owner on subcontainers and objects" - no change.  

I went to the security tab of the folder, chose advanced, and on the permissions tab I checked both the "Allow inheritable permissions ..." and the "Replace permission entries on all child object ..." options and hit Apply, but still have the same problem.

I check some of the folders within this folder and all of them seem to be larger in Treesize than when I display their properties with Windows Explorer.
In the large folders you found(how many are there?) - within those folders have you found the large files for example?

The angle I'm coming from is - Windows properties isn't showing your size correctly - but at what level? I mean as an example if I have 1 main folder and 4 subfolders - the main folder doesn't show the correct size - but 3 of the 4 sub folders DO show the right size - so the issue is folder 4...can you determine using Treesize if you have a similar issue? So check a few of the subfolders to see if they are reporting size correctly - that way you can narrow this down to the issue folder...that's the way I'd approach it at this point(since everything you've already done is correct)

Are there ANY folders that are displaying the CORRECT size(matching treesize for example)?
How many subfolders are we talking about here? 100+?

Lastly - when you reset permissions - they did take effect yes? You've checked the lower level folders to confirm? Cause from time to time I've seen issues with permissions that did not push down to lower levels...check the permissions on some of the FILES within some of these oversized folders to see if they are reporting the permissions of the folder just in case...
dcpwebberAuthor Commented:
Within the folder there are 27 folders in both Treesize and Windows Explorer.

I've checked each of the folders and only 2 seem to match.  All the others are far bigger in Treesize than in Windows Explorer.

After doing some more detective work with Treesize and Windows Explorer I'm thinking that the problem lies with robocopy and junctions.  When our users log off we have a logoff script that copies their user profile from their PC to this folder on the server for backup.  The script uses robocopy.  The users are running Windows 7 and the server is Windows Server 2003.  I checked the logoff script and it did not have the /XJ switch on the robocopy command, so I added it.  We'll see if anything changes after tonight's round of logoffs.
dcpwebberAuthor Commented:
I booted the server with an Ubuntu live disk and deleted the contents of the shared folder.  The updated logoff script seems to function correctly so I think my problem is solved.  The Treesize utility gave me the data I needed to solve this.
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