I am using ebook format (ebook3) with my section types mapped to the layout. I only have 3 types. I did rename my format so I could reuse for 2nd book I want to re-publish. But no styles appear as drop-down choice for My format under the HTML Elements pane (or any of the other drop-downs).
Oh, sorry for the lack of clarity, when I said “Ebook” compile format, I meant from the list of options in the left sidebar. You pick “ePub 3” as the type of file you want to create, at the top of the window, and then from the left you choose how you want it to look. With ebooks there aren’t many choices (like how with RTF you can choose between manuscript, modern and so forth).
You can try it with no risk, since all of your settings for your current Format are saved. Just selected “Ebook” from that left list, and click on Assign Section Layouts to choose from the many different layouts you can select from, to choose how the book will look, and see if that works better for you in general.
That aside, I don’t know what else to suggest other than to double-check your Styles list again in this custom Format.