You would lose very little by downloading and installing Sigil to see if it would help you. Sigil is a WISWYG editor for ePub books, so it could provide an easy way to determine what is setting the margins (and possibly correcting them). Some people get on with Sigil and others do not
Only caveat - make sure you experiment with a copy of the epub file so that you always have the orginal to revert to if you mess things up.