Then try to override the default CSS by using --override-css or manipulate the page/margin info i.e. --margin-top etc.
You might want to search in these forums how to override the CSS as I haven't done it myself (yet).
By the way, I have access to an iPod Touch (the wife's) but have not yet viewed .epub books thereon with stanza, so I am interested in finding the solution to your "problem".
EDIT: Great, I see, Kovid to the rescue...