I am having trouble with compile ignoring my highest level folders. Scrivener recognizes level 2 but not level 1. My section titles do not appear in the book when I compile for .pdf or .mobi. I have attached a screen shot. You will notice that in my 2.5 version while I am highlighting the top level folders in the formatting tab, they aren’t being highlighted in the binder.
Are those folders marked to compile “As-Is”? That forces them to always compile only their text, regardless of the settings in the compile formatting pane, and so those items marked “as-is” aren’t highlighted in the binder. You can adjust the “as-is” setting in the Contents pane of compile.