Compile issue re: sections not compiling properly

I had an issue with some folders and files (my first three chapters) showing their section type differently when highlighted in the Binder to in the Outliner. I seem to have resolved this but the problem remains that when I compile the whole manuscript any changes in formatting do not compile in those folders and files where the earlier problem existed, regardless of which compile format is used (i.e, I’ve tried different in-built compile formats). The allocated section types are the same throughout (i.e. Chapter and Scene) and it makes no difference if I switch between allocating section types or using ‘Structure-based’.

I can’t work out if this is a glitch or a settings issue.