I haven't thoroughly researched this entire problem but I'm using a Kobo Touch and it's annoying as hell with the bottom margins so wrong.
However after messing around a bit I got a good result using the "edit book" function in Calibre. (I believe in previous versions it was called "tweak book").
In edit book, I opened up the style.css and did a find and replace on the orphans and widows. I could see there were a lot of them in there (for the different styles in the epub) and they were all listed as 2. I got a good result from doing this - simply adding a body .. etc line didn't seem to do much. Afterwards you close the edit book function and save so no need to do the conversion.
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