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Looks like the affected books were generated using some sort of trial/unregistered version of ABBYY's Finereader OCR or their PDF-production app and it includes some promo text to try and get people to buy a copy.
If that's in the actual PDFs, you can try editing the affected pages out before you do the PDF convert. Sorry I can't point you to any Windows utilities for that, but I'm sure someone here knows of some.
As for Calibre's bulk convert, you can set mass-settings for all PDF conversions, including the line-unwrapping, via the Preferences button -> Conversions, which should then apply as default across the board.
I don't know if you'd then have to uncheck "Use saved conversion across individual books" to get it to do so, but you can experiment in little batches of two or three until you've got it all figured out.
Hope this helps.
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