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That is definitely odd. And you've said you've uninstalled and re-installed. Well, Calibre does retain some information about the plugin between runs. Before we try to edit that file can you test another plugin.
Can you try installing one of the other plugins and see if you get their icon in your preferences->toolbar to select?
And just to recheck - do you have the 'Kindle Collections' menu in the text menubar above the main toolbar? If so, when you select 'menubar' in preferences->toolbar you should see the icon in the list.
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