Have a weird issue. I am upgrading from 5.6.2 and following the documented suggested upgrade path.
As soon as I go to any version of 6, even upgrading step by step to the most recent my Site Settings for my Portal (0) like the attached screenshot. The other portals when logged in as a super user appear to be ok. It's just the root portal. It may be related, but if I use the Telerik editor on the root portal it doesn't show any files when using the image manager, and there are ton of files and images.
I have done all the obvious stuff a bunch of times: Confirmed the identity of the app pool has full access to the folders, also made sure those permissions were set to all sub-folders. I've even gone as far as giving 'Everyone' access (this is in a test environment) just to see if it works. No luck. I've also tried recursively syncing the files in DNN.
There is also an issue with the Telerik editor where it doesn't show any files or anything. I'm thinking these are some how related. But if I go to the Portals > File manager area I can see everything just fine.
Tried this too: http://www.dotnetnuke.com/Resources/Blogs/EntryId/3021/No-Folders-in-DotNetNuke-RadEditor-Image-Manager.aspx
Any thoughts or ideas would be appreciated.
I think you're running into this issue that Rob discusses in his blog
deprecated link removed, pointed to unsafe page.
Edit: Original link no longer valid. Basically the problem is that the Root folder in the portal doesn't have the proper permissions set. Try setting the "View" permissions for all users on the root folder via the Admin/File Management page.