In your html snippet the chapter heading is contained in <h2>...</h2> tags. Is there anything in the CSS which specifically references h2?
Also the <h2> tag is a child of <body class="calibre" ...> and so will (I think) inherit styling from entries in the CSS such as
Code:
body or
body.calibre or
.calibre
I'm not sure about the first 2 but there is almost certainly an entry in the CSS for
.calibre.
You could try and fix it during the original conversion by putting something like
Code:
h2 {margin-top: 0;}
in the ExtraCSS box on the Look&Feel page.