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The problem is that in an eBook there is normally no such concept as a fixed sixe page with breaks between pages. The closest one gets is a style attached to something like a heading that says "start on new page".
I have never had to convert any of my ePub files to make them work on my iPad. I can use the same ePub file on my ipad and Sony PRS-950 without any issues of the sort you are describing.
It has got to be something internal to the specific eBook you are trying to work wit, and without having it available to examine its internal formatting it is impossible to guess at the cause.
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