Have you double / tripled checked the settings in calibre?
You need to check the following:
- Preferences | Import/Export | Sending books to devices
Metadata management AUTOMATIC
- Configured either the Kobo Touch or the Kobo Touch Extended driver depending on which you are using.
Preferences | Advanced | Plugins
In the area for shelf info, type <your choice of custom column> and possibly series
Select any other relevant options. It is suggested that at a minimum you select the Create Bookshelves and Delete Empty Bookshelves options. The other options are not shelf specific.