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bartek158 - Where did the EPUB come from? I suspect it's the source of your problem, not the calibre conversion.
Could you post a screen shot of the EPUB->PDF conversion you ran? Just the Metadata panel, viz:
What happens if you remove the cover from the EPUB before you convert it to PDF? The
Modify ePub plugin can do that for you, viz:
What cover do you get if you do an EPUB->EPUB conversion, before you do the EPUB to PDF conversion - do not put anything in
Change cover image: and do not check
Use cover from source file ?
BR