Issues with Offline File Syncing

Question

Hello all,

All of our users have their Desktop and Documents folders mapped to our file server. Sync Center recognizes this and creates offline copies of these folders' contents.

Well now we have one site that is having issues. When user's log into their PCs they will only see some of their desktop icons and most will have a gray "x" on them (typically in the lower right hand corner of the icon). While in this state the desktop and documents folders are not communication with the file server, for example if I create a folder on the server under the user's desktop folder they will not see it, or if they create a new folder on their desktop on their PC I will not see it on the server. Another thing is that users also have a mapped drive to a file share that is on the same server. Typically when accessing this share a user will see a folder that is their user name (this has their desktop and documents folder in it) along with a few other folders (it varies depending on the user these folders are typically shared across departments). Yet during this time when a user goes to that mapped drive they will only see the folder that is the same as their user name and any changes made in here still don't show on the actual server. Also, it doesn't matter if you access the share via a mapped drive, or if you navigate to the server manually.

Now if I disable offline files and reboot, the issue immediately resolves. User has their entire desktop, they can see all the folders they need to in their mapped drive, etc. Now if I enable offline files and reboot again the issue is still resolved, that is UNTIL I click on the user's desktop 'Always Avaliable Offline'. Once it tries to do that initial sync it fails (it shows literally hundreds of errors) and the desktop reverts to its partial state with gray "x"s over its icons.

This seems to be affecting only this one particular site.

I have tried flushing the user's DNS cache. I have also reinitialized the CSC cache. I have tried multiple different ways to do this from registry edits, to command line, to actually clearing out the folder manually. But always to no avail.

Any help regarding this would be most appreciated.