i think what he means is, correct me if I am way off, you need to be more specific in telling calibre where the chapters are in the book. so if you have an <h2> in front of every chapter, and you tell calibre to just find <h2> it sometimes wont work, like in my case. so you then have to tell calibre to look in specific areas of the text for the h2 code. im still trying to figure it out myself. check out this link:
look at the part where it says "select by tag content". it may help you. i think the more specific you get with telling calibre to look for your tags the better the outcome. i could be totally off but i am sure that is what he means. as i said, im still trying to figure out this whole thing myself.