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Why do you start with a PDF file to convert to ePub. That's extremely poor workmanship. In order to make sure the conversion is perfect, you have to A/B compare the PDF and ePub. That means every word, every letter, every punctuation mark, every place there should be a style, every line, every paragraph. It's tedious. Not worth it.
Anyway, you should be using Adobe Digital Editions to look at your ePub and if it looks good, then it's the fault of the other programs. For example, I have an eBook that looks fine with ADE on the desktop and on the Sony Reader. But on an iPad using iBooks, the first line of every chapter has a gap between the line and the next line in the paragraph because of the drop cap. I fix this with a line-height of 0 in the CSS and ADE works. iBooks seems to ignore this and there is a gap.
So unless it's ADE, it's a bug in the program like Stanza is buggy. iBooks is buggy. So do not beat yourself up about your ePub no looking good in some programs.
But before you worry about how it looks, worry about how it converted. get to A/B comparing everything from the smallest period to every line and every paragraph. There is NO PROGRAM that will convert your PDF to ePub without introducing errors. And even ligatures can be a problem if the program that converted outputted them.
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