One thing I can think of is that the conversion will split the input into multiple files within the ePub. This is done on chapter breaks and size. Depending on how you are viewing the ePub, at the breaks, there can be extra whitespace at the end of the file. For example, the Calibre viewer will put the start of a new chapter/file at the top of a page. So, as you scroll through the book, the page before the new chapter/file can have a lot of empty space. If his is what is happening, if you scroll backwards from the new chapter/file, the previous page will appear to full.
To check the above, you can edit the ePub via the "Tweak Book" option in Calibre or with Sigil. Either will let you see structure of the book. You will also be able to see if any strange extra code has been added that might cause what you are seeing.
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