I believe, davire, you may be using spacing between paragraphs that is so huge (looks like a full empty line) that the difference compared to that intentional section break all but disappears.
Try reducing your paragraph spacing to, say, an empty half-line (that's the paragraph spacing I prefer); perhaps the section break will become more prominent then?
The trouble with switching away from publisher's mode, is you are essentially thereby giving permission to Moon+ to reformat the entire book according to your customised instructions. This usually works out fine, but in your particular book, it produced an undesirable effect.
The flaw could be in Moon+'s parsing of the book, or in non-standard coding of the book itself (just because the section break looks fine in publisher's mode, doesn't guarantee it's coded properly; for example, it could be an amateurish sequence of
<br><br><br> tags). Try reducing paragraph spacing in the book to see if it helps any.