Linda, I noticed the same thing with Draft2Digital. (In my Word doc, I use a single * to indicate a scene break, which was converted to several blank lines. Also, my left-justified first line of each section/chapter was given an indent.)
I'm pleased to report the epub is now published to Nook(less than 12 hours), Kobo(5 days) and Apple(6 days) with no trouble, and it was all very easy so I've certainly no complaints! But since this is beta, and Aaron says it might be possible to add some formatting options in the future, I'm another one who would like something more obvious than a space to mark a scene break, and ideally I'd like to keep my left-justified first line of sections and chapters.
Also, is there any way of keeping a space above and below pictures, and between occasional lines of text? I use "space after 10pt" in Word's paragraph formatting to do this for the Kindle when I upload to Amazon, but Draft2Digital stripped these spaces out during conversion. I suppose I could use a * (see above!) but the space would then be too large, I think...
Any ideas?