Sorry for my late response ...
I think the "problem" here is multitasking, which never really quits an application but rather puts it in a waiting state in the background. When you "open" it again, the app does not really launch, it is just brought to the foreground, and this is why Notebooks usually takes off where you left it before.
The setting we discussed above has its effect only when Notebooks is launched. So at the moment, I am afraid there is no way to force Notebooks to start at the top level every time you "open" it. - However if you tap and hold the book icon (the jump button), Notebooks immediately jumps back to the top level; I hope, this might be a workaround for you.