Ah, well, as I said, I never had any issues at all (I just read books; no notes, no bookmarks, just...reading). I also didn't have any other apps (apart from std) on my iPhone, so I don't know if that helped me
If I didn't use any reader because I didn't like the way it displays the index/list, I'd be still be using paper books. I've pretty much accepted that my requirements aren't "mainstream" so I just go with the flow. I've been ebooking since my Palm III, so I can cope with change and not getting my own way.