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Hey Doitsu,
I've tracked (with some help) my double mimetype issue down to this plugin. The problem stems from you writing a new mimetype file to bk._w.ebook_root (which is the actual Sigil scratch directory). It's fine (while still usually discouraged) to use bk._w.ebook_root for read-only operations, but since you need to create a mimetype file for Epubcheck, you should probably create your own temp directory, copy the book contents there -- bk.copy_book_contents_to(temp_dir) -- and then create your mimetype file.
Let me know if there's anything else you need to correct the problem.
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