Sure thing!
Go to your database and check your Folders table. It should be there as Folders unless you have an objectQualifier defined in your web.config file. This table will list all the folders that the database is aware of.
Then open your FTP site and go to Portals\n where n is the numeral for the portals under consideration, probably 0. Here you will see a bunch of folders. These are the ones created thru the Admin's File Manager tab.
Compare the listing of folders in the DB table to the folders you find in Portals\0. You may find one or more in the DB table that do not exist in the portal.
I had deleted a folder thru my FTP access, and it was still listed in the DB table. This is what causes the problems - files and folders should only be deleted thru the File Manager. If you check enough documentation, you will find this note. (I didn't until after the fact).
After this you will also need to check the Files table and compare each of the files listed in that table against the files in the Portal\0 folders. I had 3 orphans here. Again, I had deleted thru the FTP access. Again a No No.
I had 800+ files to check, so I copied the table from the DB, put theinfo into an xls, sorted on FolderID and alphabetical name, then compared. As noted above, 3 orphas,
I fixed these two serts of orphans, and all was back to normal! :-)