Hm, that sounds like it is an issue with the catalog on the Nook rather than a Calibre issue. I don't think I'll be able to help you much with that, but someone might get a clever idea if you posted a quick rundown of how you created the catalog- which format and which special options you used.
One spontaneous idea: How many books do you have in your library? I seem to remember some display issues on dedicated readers due to overly large catalogs.
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