It appears to me the underlying problem is that your 'notes' Section hasn't had its page layout correctly configured. It uses both the 'Different First Page' and the 'Different Odd & Even' settings, but you haven't unlinked all three headers for the Section from the previous Section. You'll need to do likewise for the following Section, too.

To do the unlinking, insert a couple of manual page breaks into the Notes and Glossary Sections, then make sure all three headers in each of those Sections are unlinked from those that precede them.

PS: I can't see the point of the Section break that follows immediately after the Notes Section.

__________________
Cheers,
Paul Edstein
[Fmr MS MVP - Word]