I just had to fix this and I'm running 6.2.4, though I originally installed it at version 6.2.  I think it's of note that running the script above will work, but any reference from another table that references the fileid, such as the user photo profile property or banner file will not work after you run that query.  I had to manually re-link up my banner images and I ran the following script to rematch up the user photos:

 UPDATE dbo.UserProfile SET PropertyValue = (SELECT TOP 1 fileid FROM files WHERE folder LIKE '%/' + CAST(u.userid AS VARCHAR(100)) + '/')
FROM
    userprofile up INNER JOIN
    users u ON up.userid = u.userid INNER JOIN
    dbo.UserPortals p ON u.UserID = p.UserId
WHERE
    PropertyDefinitionID = 42  -- WHERE 42 IS THE PHOTO PROFILE PROPERTY ID
    AND p.PortalId = 0

Any fix for this? 

We are running DNN 6.2.5, and it used to work. Now Portal/0 shows just empty Image Manager, another portal is ok. 

Just want to add that mine is now working correctly after I

1. used the script to rename all the folder names in lower case, clear cache and resync with recursive.

AND

2. then I noticed the folder permissions were set to deny "Open Files in Folder" and "Browse Files in Folder" for all my folders. I cleared the red dash in the check box on the folders and now the image manager shows folders and files again.

Hope that helps someone. -Mark Buelsing