Thanks for the suggestions. I've tried using folders and putting epubs in the root, neither works. I'm not an epub/css expert and don't care to be, so I won't be looking into that. My nook loads all my epubs regardless of type. My wife's kobo, the one with these problems, does not. When the $99 US refurbished nooks went on sale before Christmas, I bought 3, one for my in-laws, and one for each of my older daughters. Although heavier, so far the nooks have proven to be rock solid in comparison to the kobo.
But I would be happy to have other suggestions to try. I suspect this is a corrupted sqlite db on the kobo but don't know if I want to dive into that mess either.