Moon tries to be smart and does some formating on its own. I'm not sure why.
Look under the miscellaneous options and fiddle with some of the CSS and page settings to see if it works for you. Also if you just want to see your eBook as you format it you can see it in preview mode and it will render it as a Web page exactly as you formatted it. I don't recall however if you have to enable the preview button or it comes enable. If you don't see the button when viewing the book you will have to enable it.