Kobo wifi has slow processor and 5 way switch makes reading PDF books and documents very slow and clumsy. Kobo Touch is much better for many books but some really need larger screen and color.
When I was having the same problem your experiencing I would only load 10 book at once then force kobo to update library so it was easy to find book causing the problem.
These programs might help you find what is wrong with a epub and fix it so will work again on your kobo.
epubfixer
http://code.google.com/p/epubfixer/
epubcheck
http://code.google.com/p/epubcheck/