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This happens to me as well - it's most likely because the cover is not actually part of the pdf file - it just sits separately inside the ebook folder. Calibre is smart enough to pull the info, but iTunes is not. In fact, i've noticed that even when I try to "add artwork" to a pdf directly in iTunes, which is given as an option, it doesn't 'keep'.
If you add the cover and then convert in calibre (pdf-->pdf), the conversion should build the cover directly into the file that gets transferred.
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