Two problems: rebooting and software update

1) Whenever I try to restart, everything closes down but my OS just sits there with the wallpaper still up. It will never actually shut down.

2) I have software update setup to check daily but it never does. I always have to check it manually.

I've repaired permissions, etc. Any suggestions?

I would try to either a.) create a new user to see if the problem follows the new user, or b.) enable root access and see if you can perform a restart as root.

or,...

Start up in single user mode and run the shutdown command from the command line to see where it hangs.

Look at the console logs to see if tells you where it hangs.

Take a look at Activity Monitor and make note of the running processes that could be the cause, either third party or wrong version etc.

I'm sure software update is just timing out in the background. Try that as root and a new user as well.

I am revisiting this problem because I never solved it, I just kind of ignored it!

1) Booting into single user mode, I am able to reboot fine without a hitch
2) Logging in as another user, the rebooting problem still persists
3) Logging in as root, the rebooting problem still persists

Any other suggestions?