Information about the structure of the folders is held in a file called folders.dbx which is stored in the same directory as the e-mails (Inbox.dbx etc). Check that folders.dbx has not been set to read only.
If you delete folders.dbx a new version will be created based on the existing list of folders. If your folder structure is simple and you don't have any duplicate filenames (e.g. folder named Work in directory 2005 and another named Work under directory 2004) then you will probably be OK deleting the folders.dbx file.
BACKUP FILES BEFORE YOU TRY THIS!