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My suspicion is that you were using the KTE driver and sending the ePubs to your Kobo as kepubs. Your new setup is sending ePubs (the Adobe synthetic page numbers are pretty much a dead giveaway. To get rid of them, Settings => Reading Settings => remove the checkmark from Show Adobe EPUB page numbers.
You may also want to look at KoboPatch and the Unify font sizes patch to match the font sizes in kepub and ePub ebooks more consistent.
KTE = KoboTouchExtended
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