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Try switching drivers. If you are using the KoboTouch driver, ue the KoboTouchExtended and visa versa. Also make sure the other driver is properly configured for collections.
And one other thing to make sure if is that in Preferences > Sending books to devices that you have Metadata management set to Automatic.
Check the driver to make sure it is correctly configured. Under the Collections tab, make sure that Create collections is checked and that the correct column is specified. I have tags as the collections column.
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