Are you referring to the "Annotations" plugin, or the "Fetch annotations" function that is on the menu of the "Send to device" button? I can't help with the latter.
If it is the Annotations plugin, it should be working. For a Kindle, it has to match what s in the clippings file with the books and then prompt to confirm which book the annotations belong to. If this isn't correct, then I need to see a debug log to try an work out what is going wrong. Run calibre in debug mode (right click on the preferences button and select "Restart in debug mode"), fetch the annotations an post the log in the Annotations plugin thread.
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