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Set up an experiment.
Created a batch file and ran conversion from command line.
Noticed that PDF plugin sends message to output: Top margin is too small for header, increasing it.
Experimented with top margin value and found that at margin>=36 pt this message disappears.
Than I commented out header option in batch file leaving top margin at 36 pt and obtained page text shifted down to exactly the same distance as it was when header was activated.
May it be that Calibre overreacts to header presence and forces top margins to the value (36 pt) that exceeds actual height of the header?
That could be the cause of those extra space.
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