I have noticed there is a bug at least with the “start section on” settings for layouting. It goes off-index if you use inline page break anywhere in your text. This causes page breaks to appear even middle of section text as the inline break activates the “start section on” even though it’s technically still middle of rendering current section. Problem is fixed if you split text into multiple documents (and adjust the layout for different documents) and never use inline page break. Maybe you have inline page break somewhere?