Thanks for the suggestion. I think my problem is a more deep seated, and pathological problem. I have spent over an hour trying various combinations of section breaks, and that has no influence at all.
I did, however, discover that the page numbering does have an affect. If I let page numbering run unbroken from the start it has some affect. But that defeats the whole idea of using section breaks. There seems to be some bug in this at a particular place in the document. This only happens between the first and the second chapters. The way the pages flip over when scrolling is very bizarre. I think I will try to do this in Pages instead. I will report back if or when I find a solution.