i was looking at this earlier today to try and find a way to fix this problem on my girlfriend's macbook pro.
you could open system preferences from the dock just fine, but when you went to the apple menu - it would try to open, and the system preferences would show up as a default icon on the dock for a split second, and then crash.
i repaired permissions.. and then rebooted (just for safe measure)... the problem was not fixed
i ended up opening the console - and then trying to open System Preferences from the Apple menu.
it relayed to me a crash error. i wish i had it copied to show everyone - but it basically said that it couldn't find the System Preferences.app.
I had noticed that she had a System Preferences icon on her desktop, so i checked the applications folder - and there it was. the default icon. When i tried to open it the same thing happened. it crashed.
i ended up trashing the file (after entering the Admin password) and then dragging her desktop icon of System Prefs back into the Applications folder.
That fixed the problem!
i assume she dragged the icon out at one point in time, and OS X's Apple Menu had the selection Alias-ed/Shortcut to it.
you'd think that if you had a permissions problem, System Preferences wouldn't open ANYWHERE. so repairing permissions may not always be the problem
check out the console again.
