It seems that if the "On application launch reopen previously open documents" preference is enabled it works even if you launch NWP by double-clicking on a Nisus document rather than by launching it directly from the Finder or the Dock. Which is fine I guess, except that in that in the former case it opens the clicked on document first, then it opens whatever document(s) were opened previously and so the previously open documents windows end up on top of the window of the document the user clicked on to launch Nisus. If the windows overlap sufficiently, and the user is sufficiently, ah, new, it looks like Nisus is possessed and is opening documents they didn't want! And the one they did want they fail to see because it's window is buried beneath the old document window(s). I just spent a lot of time on the phone sorting out a friend's Nisus problem that turned out to be caused by this behaviour.
I think that if you're going to open previous documents even when Nisus is launched by double-clicking on a document you should have Nisus open the clicked on document last so it's window opens on top of the windows of the previously opened documents. And this option should not be set on by default (my friend assures me she didn't switch it on so I'm assuming Nisus comes with it on by default nowadays), it's way too confusing for inexperienced users.