One kepub I'd purchased from the Kobo Store was messed up, in that it'd skip erratically between chapters/sections out of proper order, making it impossible to read the book. When I downloaded the Adobe ePub from Kobo the book worked fine. If I were a less technical person I would have been really upset about that.
I really don't see why they bother with kepub at all. The chapter page count is annoying / much less useful than how generic ePubs are handled, plus the possibility of show-stopping conversion bugs like I experienced above.