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I would suspect that your epubs are error ridden, very often an gorched ToC can cause the issue you saw. Have you used either calibre's editor or Sigil with their respective epubcheck plugins to check for errors? There are also online epubcheck sites such as the one supported by ebookit.com (the IDPF validator seems to be offline) though I am always a bit nervous about uploading epubs for validation.
Another question is what site you downloaded those epubs from? Quite a few pirate sites have little concern for the quality of their ebooks and you did not mention any legitimate site such as Kobo, Google, Gutenberg, Standard Ebooks, etc. you downloaded the epubs from.
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