It would be interesting to find out if something like that is happening, because it would imply that nickle is saving its state somewhere along the way. I'm fairly certain that it is nickle though, since everything in the initialization scripts is very linear and doesn't appear to preserve any state or a command queue.

It'll probably be a non-issue when koreader is more robust anyhow, since it'll make sense to remove nickle from the works altogether. As you said, it supports more file formats. It supports organizing ebooks into directories, which a lot of people demand (and I prefer personally, no matter how much I think it would be a bad design decision for Kobo), and the PDF viewer is just plain better than Kobo's.