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My guess is that your pdf has page headers or footers in it that need to be removed using the remove header or remove footer options.
PDF chapters are detected heuristically, and this can lead to false positives in some cases, particularly with page numbers. The Heuristic code was just enhanced to detect that sort of false positive and discard it, so the next release will probably fix the problem.
That said, since it is most likely page numbers causing the problem you should try the remove/header footer function and re-convert.
If you don't think it's page numbers open a bug on the tracker - bugs.calibre-ebook.com. Attach the file and I'll take a look at it.
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