Claire sent me the document. I used the Word Toolkit for Advanced Management of Word Headers and Footers.
It made it easy to see what was going on, but does not work on a Mac.

One thing I noted was that many of the Section breaks were there to change the header text to match the content of the chapter. This is best handled using a StyleRef Field.

Other section breaks were needed for layout change and that was where the problem came in. There were some that had no displayed header or footer but where the settings in that section for the header caused a problem in the next section.