You indicated you were using ems to size your chapter headers. Pts are rarely a good choice for font size.
What does your "Title" CSS look like (that is producing what you expected) by comparison?
EDIT: also, in addition to seeing the both the "Title" and the "Chapter" CSS, it would be helpful to see snippets of the html where the CSS is being applied (for both the Title and a Chapter heading). Making sure there are not two separate CSS classes being applied to one html element is the first order of business when trying to figure out why the Previewer/kindlegen isn't producing the styling you expect it to.
Last edited by DiapDealer; 08-07-2012 at 10:38 AM.