I'd guess that side margins are specified as a percent. According to the CSS specification a percent side margin is sized relative to the height of the element (which in the absence of more information could be the screen). Maybe in scroll mode the height is the whole book or chapter, which then makes the side margins larger. (Ignore this, it's actually the other way around.)
I don't think there's an automated solution to fix that and only that. But if you know the basics of CSS and peek into the book's code, it should be relatively easy to find and fix the offending rules (I usually remove all side margins in <p>, and <body>, and add a 2mm margin in @page).