Don’t worry, your Kindle Mate is still working right. 🙂
Every time you click on Auto-Sync (or press the shortcut F2)，Kindle Mate will import all your newly created clippings and vocabulary words as well, which don’t exist in the Kindle Mate library.
When you make some changes (deleting some duplicated clippings or changing word learning status) in Kindle Mate, all the changes take effect within the Kindle Mate library ONLY. If you want to ‘sync’ those changes back to your Kindle, please use the feature Sync Changes to Kindle (shortcut F10).