I think what Bert (and Wendell) are trying to emphasize is the difference between "logging off" and "shutting down" AC. We think it is rarely appropriate to close or shut down the program. Instead, go to logoff in the file menu, or hit ctrl-L. The "still running" problem only occurs for us when the program is closed completely; it NEVER happens after logging off (and you are looking at the log in screen).
Of course if your computer is shut down, or for some reason restarts overnight....then you lose the benefit of logging off and you may still have this problem. Can you make sure your computer doesn't restart overnight?