My Mac Mini Won't Shut Down Properly

I recently upgraded to 10.6.2 after buying a mac wireless keyboard and magic mouse. Now I keep getting this problem where the OS won't shut down.
One of the symptoms is that when I move the mouse to the area at the top right of the screen with the clock, volume and wifi icons (is there a name for that?) I just get a spinning beach ball. The clock has stopped too! Also the volume controls from the keyboard don't work any more, even the remote control stops working. I can't shut down or sleep the computer, even 'about my mac' doesn't work.
Other applications seem to work OK and in Activity Monitor I don't see any unresponsive apps.
This hanging doesn't start straight away and two things that have set it off have been using the volume controls and when I tried to press ⌘-space to search for something.
I really don't know where to begin!
Message was edited by: beardiebloke

Still doing it! I disconnected all the USB peripherals and that was fine for a while, also removed stuff out of the task bar thing that I wasn't using.
Then re-connected the USB hub and it happened again... maybe it's something to do with that or just bad luck...

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    14/07/2010 20:20:29 com.apple.diskmanagementd[213] XML representation doesn't match true boot preference
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    14/07/2010 20:33:59 com.apple.launchd.peruser.501[115] ([0x0-0x19019].com.apple.systempreferences[198]) Exited: Terminated

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    Drive Genius…
    http://www.prosofteng.com/products/drive_genius.php
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