Stop reopening windows on restart

OS 10.8.4 on iMac 2.8 i7.

System will often -- but not always -- will reopen apps & windows that were open on shutdown, even though "Reopen windows when logging back in" is unchecked. Also makes for long shutdown and startup times. Very annoying.

Is there another "feature" that turns this on somewhere else besides the shutdown dialog? Or this is bug or permissions problem?

Welcome to Mac-Forums..

Can you go into System Preferences->Accounts->Login Items for your user account and see what items have a check mark against them, those will start/launch with each system boot..minimize that list to ensure a fast boot up..

And when closing down make sure the re-open button is not selected.

One other possibility: if you are not properly quitting programs but just leaving them closed, the computer might be re-lauching the programs on restart and of course they're going to open up a new default window.

Ok as chas m suggests make sure you actually choose Quit to close programs and not simply hit the red button which merely shuts the window.