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@A Lurker - if it doesn't exist, an author folder is only created for the first author name of a book. So, if you add a book by "John Smith & Jane Doe", both authors will appear in the tag browser but there will only be one author folder named "John Smith". And that's been true since i started using calibre in 2012. This linkages between a book and its authors is maintained in the database, not the folder structure; it's just a convenience store for format files, display covers, and metadata backup files.
I don't use MOBI files on Kindles, so I can't help with the main issue.
BR
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