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Unable to access some subfolders while using VPN connection

We are a Server 2008/mixed Windows XP/7 environment. I have a remote user that VPNs into our network to access network resources, one of which is a network share. When he remotes in, he can access the resources and the network share folder that I have given him permissions for; however, there are two folders he cannot access even though his permissions are exactly the same on all the folders.  

Not sure if this is helpful: This is a new notebook running Windows 7. I had it here in our offices, set VPN up, tested it logged in as the user and everything was fine; then, sent it to the user. He needed other folders available so I updated his permissions. The folder structure is:

Network drive (has access)
  Folder1 (has access)
    Subfolder1 (has access)
    Subfolder2 (has access)
    Subfolder3 (originally had no access, now has access)
    Subfolder4 (originally had no access, has access)
    Subfolder5 (originally had no access, now has access)
    Subfolder6 (no access)
    Subfolder7 (no access)

Tried creating a test folder and he couldn't access that folder either.

I checked to make sure he is not working offline and manually tried syncing the folders but it says it is not available or he may not have the correct permissions. I also tried flushing his DNS cache.

I had him try logging off and on and also restarting his computer. I'm wondering if it's something to do with caching.

Not sure what to try next.
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Are the folder names very long, such that the entire path is over 240 characters?  If so, that may be causing problems.
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Thank, Shift-3, for your response. Some of the folders he can access have longer names than those he cannot so I don't think that is the problem.
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I still need help with this. Anyone?
See if you can get to the laptop and try the following:

With a local connection (not VPN), delete the folders and be sure persistence is removed (NET USE Z: /persistent:NO and then NET USE Z: /delete. Do this for all the folders.

Now connect up with VPN and try to map Folder1 with NET USE Z: \\server\folder

Does that help access to the subfolders?  ... Thinkpads_User
Does it work with caching/csc/oplocks completely disabled?
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thinkpads_user: thanks for your reply. Do I delete the entire share from the users computer? Also, I'm assuming I substitute the "Z" for the share I created (in this case "Q").

gheist: can i get a little more info? i'm not sure how to disable "caching/csc/oplocks".
@ipsbend  - Yes, I would delete the entire share (in terms of mapping drives) from the user's computer. Make sure NOT persistent and then start again.

Now in terms of standard Map Network Drives, "Z" was just my placeholder, so Yes, substitute "Q".

... Thinkpads_User
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thank you. i will try and get access later this morning to this users notebook and will update this ticket.
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i want to clarify: "With a local connection (not VPN), delete the folders and be sure persistence is removed (NET USE Z: /persistent:NO and then NET USE Z: /delete. Do this for all the folders."

do you mean i will have to run this on subfolder1, subfolder2, subfolder3, etc., backing my way up to the share drive; or, can i just run the command on the share drive?
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Q!!! Do you use DFS? DFS with NAS?
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thinkpads_user: will do and do realize it is a process of elimination. i really appreciate your help. i am hopefully accessing the notebook remotely around 11a PST.
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gheist: thank you for your response. forgive me but i am unsure of what you mean by "Q!!! Do you use DFS? DFS with NAS?". i mean, i understand what DFS and NAS are but don't understand the comment regarding the drive letter. please clarify. thanks.
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thinkpads_user: I am getting an error "system error 67 has occurred. network name cannot be found" when trying to run the net use commands. i am not connected to the vpn as you instructed.
Do you use DFS (Distributed filesystem of Windows, locating different directories on different servers or Network Attached Storage devices)?
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the shares are all on our server and not a NAS.
If you are getting a "name not found" error and connected directly (not by VPN), then you have a DNS problem of some sort. It will be helpful for gheist to chime in here.

Let's be very clear here: In your last post, you are connected directly to your server when you say you are not connected to the VPN. ... Thinkpads_User
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i may have misunderstood. i am looking at the users screen via a gotomeeting session. i have disconnected from the VPN and am looking at the users computer. I just did an ipconfig /all command and it looks like his wireless NIC is still pointing to our domain settings, i.e., his ip address is 10.0.0.xxx, his default gateway is pointing to our LAN router. Shouldn't it be pointing to his local network settings if he's not connected to the VPN? I did an ipconfig /flushdns. but it is still pointing to the domain settings.
"Name not found" could be exactly a sign of DFS redirection impacted by DNS omissions.

Please run diagnostic tools as described here:
http://support.microsoft.com/kb/265706

Please share their logs with your Server/Active Directory support before coming back to us.
They may have better ideas about network layout and/or which data in logs is your company secret...
Also it is a good idea to run both diagnostics at home and in the office and compare logs after.
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ok. so, are you instructing that i run the diagnostic tools on our server and also on the client machine?
Emphasis on "compare" part - you miss something from DNS at home (which is probably found in NB naming in the office. So tools are bigger than problem but will show the difference...
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thank you. i just took a quick look at that link. there is a lot on that page; i haven't used many of the diagnostic tools. do i need to do all of them or is there a specific tool?
Another test to try is to turn off (disable) the wireless connection and hook the machine up by ethernet. That may help clarify the issue. ... Thinkpads_User
You need to run two tools down-loadable at the end of page logged in with same rights, then share logs with your admin before sharing with us.
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gheist: ok, i see that. but do i run every single one of those tests? currently, i am not experiencing this issue with all of my remote users though I may be having an issue with one other. thanks for your patience.
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thinkpads_user: i had meant to try this and forgot. i have instructed the user to try it and let me know what happens. thanks.
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Hi thinkpads_user: connecting to a wired connection appeared to work though I'm not sure why. This is what the user emailed to me this morning:

"... noticed this morning that when you click on a folder ( not double click) there are more options that now appear across the top of the window where the "Organize - Open - Include in Library - Sync...." menus are...because after I just clicked on a folder I saw new menu items appear up top such as " Burn - Work Online - New Folder - ", well, once I saw the "Work Online" I clicked on it and it made all the folders available.  I then restarted my computer, disconnected the wire and connected via wireless, and was able to still have full access.  Not sure why those other menus didn't appear, but they do now!

It appears that the options didn't appear until after he connected to the wired connection and, my being fairly new to Windows 7, am still learning OS and didn't recognize anything was missing. Can you tell me how the wireless setting would affect those menu options and how I can prevent this issue?
@ipsbend - the use of public wireless can alter and change things. That is the "how".

1. Look in windows\system32\drivers\etc for the Hosts file. Look in this and see if there. The default entries are all commented out.
2. Look in the wireless manager (Windows or other wireless manager), remove all the profiles (delete them all).
3. Look in network properties and do a repair of the wireless connection.

Now restart the machine, add one wireless connection (work I presume) and see if it works. It may be necessary to again delete all wireless profiles and then uninstall and reinstall the wireless driver.

... Thinkpads_User
I forgot. Also look in the properties of the wireless connection. Automatic and Proxy may have been checked. Be sure to look there and uncheck these things. ... Thinkpads_User
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thanks. will try this. also, this user is 100% remote and doesn't use our office wireless network. that being said, when i set up the notebooks in our home office, i test the wireless connection and also the mobile broadband wireless we have thru verizon so the profile is still in there. how about if i remove everything except his home office wireless network? also, i believe that when a computer connects to a workplace VPN, it changes the IP settings. i also thought that once disconnected, it should revert back but this user's settings didn't change. am i incorrect about that?
i believe that when a computer connects to a workplace VPN, it changes the IP settings. i also thought that once disconnected, it should revert back but this user's settings didn't change. am i incorrect about that?

I use IPsec VPN mostly, but I have also used PPTP VPN as well. My wireless settings were never changed. VPN rides on top of your network structure, so I do not think there should be any changes there.
... Thinkpads_User
It is something about DNS - diags will tell.
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thanks! fyi i am out of town for the next week and can't run those tests until i return. i will update this ticket once i have done run the diagnostics.
The asker needs to respond here. We have given a lot of good solution-driven information here, but if the asker cannot make it work, they need to say so. ... Thinkpads_User
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Sorry! I meant to update this last week and it slipped my mind. The folders are working correctly now. This is what the user sent me:

"I had not noticed before, but just noticed this morning that when you click on a folder ( not double click) there are more options that now appear across the top of the window where the "Organize - Open - Include in Library - Sync...." menus are...because after I just clicked on a folder I saw new menu items appear up top such as " Burn - Work Online - New Folder - ", well, once I saw the "Work Online" I clicked on it and it made all the folders available.  I then restarted my computer, disconnected the wire and connected via wireless, and was able to still have full access.  Not sure why those other menus didn't appear, but they do now!"

So, because I am new to Windows 7 Pro, I am still getting used to how things look and where I go to find stuff. I'm not sure where I went wrong and how I missed the options for Working Online, but I think after I updated permissions I should have disconnected and reconnected to the share which I thougt I did, but guess didn't.

Thank everyone for your assistance.
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I'm choosing this as the answer because I don't think it was a dns issue. I believe this answer would have eventually led to the resolution.
Thank you, and I was pleased to assist. ... Thinkpads_User