Well, a quick check shows that for some reason the cover wasn't resized when I batch processed the files, unlike all the other pages. Not sure why not, but I've resized the cover and deleted and reuploaded the file. If nothing else, it instantly fixed the thumbnails on the other issues.
For those of you who already downloaded the book, I wouldn't bother changing versions. The only difference is the smaller front cover, and since the old one works fine otherwise there's no need.