Have you looked to see if you have elements with bottom-margin being applied (via css or otherwise) where the blank pages are occurring?
If not, it sounds like that's just the luck of the draw in ADE (depending on line-height, font-sizes, etc...) in where the last line of a flow happens to appear on the screen. Using top-margin for vertical spacing instead of bottom-margin sounds like the best way to minimize the chances of it occurring. Though ADE has different issues with top-margin not always being honored under certain conditions as well (namely following "soft" page breaks).
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