If I understand you correctly this is a known issue (publisher settings set the fonts at a higher level of specificity than the userstyle sheet is overriding to set the fonts) - also by 'your books' you mean books that you are reading rather than books you are writing.
If so then this is fixed in the NookTablet, will be fixed soon in the NookColor and will most likely be fixed in a future ( after 1.1 ) update to the the Nook STR
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