I'm perplexed and hoping someone can help with this. When I shutdown mountain lion by clicking on Shut Down... I get the dialog box that has the Reopen windows when logging back in button unchecked. No problem, when I reboot my windows do not reopen. But if I use shutdown from the command line, or use applescript to shut down: tell application "Finder" shut down end tell My windows open up on restart. In Lion there was a box in preferences about reopening windows but I don't see the same thing in ML. Does anyone know how to modify this behavior in ML?