This sounds as if you used calibre to convert the PDF to an "ebook format", like Mobi. That is more an issue with Calibre usage, rather than a Kindle developer topic. Calibre has a vast amount of settings regarding conversions. Some of them might help here... Sorry, I can't really help much more. Maybe - as this is a DX - you want to try and put the PDF on the device without conversion. Again, this can be configured in Calibre somehow - but I don't use Calibre, others might have suggestions.
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