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The Calibre metadata search and browse by tags/series features list search results based on the .metadata.calibre file, which is supplied by Calibre and should contain the metadata of the files transferred. In your case, there seems to be a disconnect between the data in the metadata file and the actual books transferred. However, I'm not sure what could be the cause.
Have you tried doing a wired transfer and see if that works correctly? If it does, the issue must be somewhere in the wireless set-up.
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