OK, forget everything I've said
I just learned from the first page of the topic that PDF can contain tags. I've been learning PDF stuff through the Poppler code, which is used in Calibre for PDF conversion and doesn't make use of tags at all. That's probably why Mobipocket Creator is so much better at PDF conversion to Mobi for PDF files that are properly filled with tags.
http://www.planetpdf.com/enterprise/...ContentID=6067