When you have your Clara HD connected and open Configure this Device from the device dropdown menu, what you see on the second tab (Collections, covers and uploads)? Is the Collections check box checked? Is your custom collections column in the Collections columns box? Is Create Collections check box checked?
After you send the books to your Clara HD, did you eject it and then reconnect it so the metadata could be updated? The first connection sends the books which your Clara HD will import after the safely eject. This places the ebooks into the database so the entries can be updated on the second connection.
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