You might want to try the new paged mode for reading your ePubs and see if it's to your liking and makes a difference.
Release: 0.8.61 [20 Jul, 2012]
E-book viewer: Add a paged mode that splits up the text into pages, like in a paper book instead of presenting it as a single column. To activate click the button with the yellow scroll icon in the top right corner.
In paged mode, the ebook viewer no longer cuts off the last line of text at the bottom of the screen, and it respects CSS page-break directives. You can also set page margins and control the number of pages displayed on screen by clicking the Preferences button in the viewer and going to 'Text layout in paged mode'.