Originally Posted by Mrs_Often
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.
So, if I am understanding correctly:
1. Factory reset
2. Hook device up to computer, wait for Windows to recognize it
3. Transfer 1 book to device
4. Eject from computer, allow device to update
5. Attempt to open book on device
6. If book opens correctly, attach device to computer again
7. Repeat steps 3 through 5 for all books.
All of the books on the device are the same ones that were on it previously, when it was working correctly.