I have been tearing my hair out all day with the same problem.
steve2112 - you can try "style mapping" and map styles to tags. It's under the fly-out menu in Paragraph Styles. Useful video here:
http://tv.adobe.com/watch/learn-inde...d-epub-export/
This has helped me a bit, in that it has standardised the spaces. But for some reasons I can only apply spacing to paragraphs (p tags in xhtml) and not to headings (h1, h2 etc in xhtml) used in epubs.
I've even tried editing the .css in the unzipped epub files but that doesn't work either.
Stopping while I still have some hair.