Sorry for replying to such an old thread. I found it with Google...
Same issue for me; for several books from the StoryBundle Fantasy Bundle (the Christopher Bunn ones), my reader gave me huge margins even after conversion, which wouldn't go away despite all filtering in Calibre. Using the Tweak Epub feature, I finally found this page-template file to be the culprit; deleted it and all is well.
In the content.opf it's specified like so:
Code:
<item href="OPS/page-template.xpgt" id="pagetemplate" media-type="application/adobe-page-template+xml"/>
the media type differs from the one calibre is looking for. It SHOULD be application/
vnd.adobe-page-template+xml but apparently, the ADE reader software itself isn't picky about it.