Calibre is only as good as the source document. If the PDF has some nasty coding in it, the epub conversion is not going to do away with that on it's own. You have to get into it and look at the coding. You can do that by opening the "search & replace" feature and look at it, then compare that to an epub that was not made from a PDF. That will give you a good idea of what is wrong with the hidden parts of your doc.
Also if you have opened a screwed up book, even just once, then go on to read other books, that screwed up book can still cause problems on the device. Delete it, and you might even have to restart. Worse case scenario, you might have to reformat the Sony. I had it happen to me. Lately I've been checking everything through Sigil (via the Calibre plugin) to see if there is anything obvious, before I put it on the Sony. (That's a great way to remove the excess image files that are often included in romance novels).
Last edited by booklover6; 02-09-2013 at 08:58 AM.