Are you using a sideloaded font? As I recall there were a couple of sideloaded fonts that caused huge amounts of whitespace--as in a half of a page in some cases. You wouldn't think it would be a font issue, but that is what the Kobo devs told me it was. Even with system fonts I occasionally saw page breaks that resulted in several line heights of white space. But that was back in 1.9.6.