I recently had the problem with cut-off text in one of my kepubs. It was just one book, and it didn't matter if I had headers/footers turned on or not. I ended up reconverting from ePub to ePub in Calibre and then transferring to my Kobo Aura HD with the extended Kobo driver. After conversion and retransferring, the resulting kePub on my HD worked perfectly.
That being said, I like having the header and footer on, so I don't see the problem with cut off text when these are turned off.
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