Originally Posted by melabonbon
Ejected the device, it told me it was updating, then about halfway through the screen turned entirely black.
I think that is a big part of your problem. If it crashed in the middle of processing new books, it means (a) there's at least one 'bad' book in there that Kobo isn't happy with and (b) the processing wasn't completed, and not all books on your device will have been properly added to the database. This could cause blank pages and such things.
If I were you I'd do another factory reset, but this time, only load one book at a time. It might be very time consuming, but at least you can confirm that each book is accepted by the Kobo, until you come across one that isn't.