Well, thanks to your tip about the bad e-books, I reloaded my wife's library in chunks and managed to track down the culprits. It turns out that there were several bad books, all from the same series, so I guess I just managed to find a badly done collection, or had a bunch of downloads go awry.
I used the built-in e-reader in Calibre to verify the books, and it reported the invalid state on each one. I know now to use this approach in future, whenever I have books of dubious quality.
If you're still interested, I can send the books to you, but I think it's likely to be a waste of your time.