From reading B&N's nook forums, it looks like this is a known issue with some books in the current (1.1.0/1.1.1) firmware and is expected to be fixed with the next release - which supposedly is coming out before the end of the month. Personally I haven't had any issues on the three books I've read so far (1 ePub I sideloaded, one ePub I bought from B&N, and one PDB I bought from B&N) on my nook, but it does seem to be a fairly widespread problem.
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