Keep in mind that there are many ePub reading systems out there and that you can't necessarily make something that works perfectly on all of them. Some ebook designers prepare slightly different ePub source depending on the target platform (iBooks/webkit, Adobe RMSDK, etc.)
It's even worse than that because even within the Nook (or Kobo) platform there are at least two rendering systems in play (Adobe's SDK is only used on Nook devices, not in the mobile and desktop apps). It's very similar to web development in that what works well on one browser doesn't necessarily work well on another one.
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