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@diremommy - post the contents of the log that appears after creating the collections into a post here between SPOILER tags and I am sure someone could point to what is wrong.
You say you are putting some books into some collections manually on the Kindle? Have you made sure to not having some naming convention conflict to prevent the calibre plugin from overwriting them? Also have you ticked the box saying to preserve Kindle only collections? State some examples of collection names of both what you are manually creating, and what you are having the plugin create based on tags along with the log output.
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