I think you already have your own solution.
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Since the other .pdf books I transferred seem to be fine, my guess is that I should try to convert the rogue books to epub (or whichever is the most trouble-free format for the Nook -- would like advice) and then transfer again. But I'm still curious why this is happening and if there's a fix short of converting.
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In my experience reading books on my iPad and Nook is I try to avoid .pdf format if at all possible (especially on my old Sony PRS505). PDF's are basically pictures of a page and are not "reflowable". Which is to say, they cannot have their type size changed or adjusted to the reader.
So, I would attempt to change ALL fiction books possible to epub's for the Nook.
Books like "Mastering Regular Expressions" (a computer tech book) have many type changes and special characters and don't take well to being converted to epub. You lose all the formatting of a "for dummies" book for instance. I leave these books as pdf's and view them on my iPad or computer. For these reasons and the limited size of the Nook's screen I haven't even attempted to read a pdf on the Nook.
The best thing about epub is you can resize or change fonts to your liking by most readers. PDF's can't do that but they work good for magazines or comic books.
You didn't say but if you have a Color Nook the pdf's would certainly look much better for magazines and such. Otherwise your profile just says Nook and the B&W of the classic Nook will not render magazines and pictures very well.
Happy Sunday
Archon