See the attached PDF file and notice the "Chapter 2" section page numbers are crossing over into the "Non Rule Section". This appears to be a bug in Prince as best I can tell.

I've also attached the HTML and CSS files used to generated this test.

1. Numbering Issue.pdf‎ 87.9 kB ‎
   PDF
2. NumberingIssue.xhtml‎ 99.6 kB
3. render.css‎ 11.5 kB

It looks like the footer definition for that section occurs at the end of the section, not the beginning, so the footer isn't changing until right at the end.