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If the PDFs have headers and/or footers, they will show up in the resultant mobi text itself. For example, page numbers from the PDF file will be show up i the actual text when reading it on the device. Calibre lets you specify regular expressions that it uses to try and identify the header and/or footer and remove it from the conversion.
Personally, I haven't been bothered too much by these extra bits and just do a simple pdf->mobi conversion when I need to.
Mitch
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