An ePub book
can force a font that is included within the ePub file if it wants to. This is useful for ePubs written in, say, Russian or Korean or Greek. The NOOK doesn't contain a variety of languages in its fonts.
Unfortunately, some English-language e-books abuse the feature and do the same. If the e-book doesn't have DRM you could put it into an ePub editor and fix that, but it's probably not worth the trouble and the e-book probably has DRM anyway.
This is covered in the NOOK manual (bottom of p. 111 in my copy of the 1.3 manual):
EPUB Format: Content is displayed using fonts embedded in the EPUB file if present. If fonts are not embedded, content is displayed in the text font you choose in the Reader.