I know Apple messed around with the window resume features in Mountain Lion (and I have it set to close windows when quitting an application). I also have the checkbox to restore windows when restarting/shutting down UNchecked. However--and I particularly notice this when I quit Calendar, Mail, and Safari, and then restart the system--upon restarting, Safari, Mail, and Calendar (or whatever other programs I was last using) open. Even though I quit them before restarting, and even though the box is not checked. Anyone else having this issue, and maybe know of a fix?