This is just a guess, but I suspect this might be caused by the text being contained in a single cell in a table. The Kindle isn't very sophisticated in how it handles tables, and if a table cell contains more text than will fit on the screen, it doesn't carry it over onto the next page as far as I know.
If the table is being used simply to control the layout, I'd recommend removing the table formatting, and replace it with simple paragraphs.
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