Section headings can be left "orphaned" in the PDF output. The section title is the last line on the page, then the first paragraph begins on the next page. This obviously doesn't happen for every section, but it does happen consistently in every manual. See page 30 (page 14 in numbering) in the Certificate System admin guide PDF. http://www.redhat.com/docs/manuals/cert-system/7.3/pdf/Administration_Guide.pdf
This is due to a deficiency in FOP 0.20.5. I will test a newer version of FOP, however this will probably take sometime to test.
Switched to FOP 0.95Beta, which fixes this issue.