Perhaps the margin is set in a style in the head section of the xhtml (html, xml, ...) file. It must be set somewhere in the ePub.
You might give the Kindle Previewer a try. Dragging and dropping an ePub on the Kindle Previewer with generate a MOBI file using its embedded KindleGen. I've found that this ignores margins set in the ePub.
Kindle Previewer (and other stuff) is available on this page:
http://www.amazon.com/gp/feature.htm...cId=1000234621