StartupShowDBWindow can change the value of the check box under current database, but for me in 2010, it doesn't seem to have any affect. I've restarted the db, with that check box set to 0, and the nav pane is still there.
edit- Okay, clearing that check box does hide the nav pane when I open the db, but only if there is no form that loads on startup, either by the startup form option or by an auto exec. When a form does load on db open, the nav pane is there. Any idea?
edit-Nevermind, I'm just an idiot. Setting this property works as expected.