USE BOOKDESIGNER instead of Calibre. Calibre is a horrible tool to convert PDFs. BookDesigner makes decent conversions.
Forget Calibre, it is way overhyped. I had so many problems with it, that I uninstalled it a long ago and I am not looking back. Judging from your problem, it has not improved ever since. The developer keeps adding features while basic functions do not work properly.
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