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I had exactly the same problem with the entire 0.6.x series (I stopped using 0.6.x and reverted to 0.5.6 in August). I would take an html formatted book, use calibre to convert it to epub, and then the book would be broken on my PRS-505. I would be able to page through some of it, but eventually it would give me a read error and would break the book (page 104 on one book, page 27 on another - but everything I tried was broken somewhere). Once I identified which book was broken where then I could reproduce the error consistently. I could not jump past the problematic page. I dug around in the epub a bit and found that it was always happening on chapter breaks, which calibre 0.6 defines differently than the 0.5 series, though I couldn't figure out what it was about the chapter breaks that broke it. I'll be back home in November and will see if the new builds of the 0.6 line solve the problem, but until then I have reverted to 0.5.6, which produces working epub output for my 505 on the exact same html input that resulted in broken epubs with 0.6.x.
So the original poster might not have funny html markup in his document, he might be experiencing the same thing I did.
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