I shut the computer down (as far as I know normally) and when I start the box back up it re-runs the entire MCE setup wizard over again losing all of my configurations. What gives? And how do I backup my config in case something like this happens again. Also, what is the best, correct shut down procedure?
I don't know why it would re-run the AV Wizard upon bootup, but to shut things down...
Power -> Power OFF m/d
How you get to the Power menu differs depending on which UI you are using...
With UI2, the green media button on the remote (or F7 on the keyboard), far right pull up menu, up to Power...
With UI1 it's just Power -> Power OFF m/d from the main screen.
It should shut the power off on its own.