I'm having quite some problems with the Dock app, that indeed reflect on all users: sometimes the shelf isn't showing, sometimes the default ML wallpaper is showing instead of my custom, sometimes I see Lion indicators. I blame the Dock app, from what I see.
You can try killall Dock within Terminal, Repair Permissions...
I ended up running the ML updater again, after which my system sound preference pane was grayed out like your Dock pane.
Sometimes it 'just works' though.