Recently I’ve noticed that my Preferences started behaving strangely. Only main panes would open, but no secondary windows would work. For example I could open network preferences and delete all interfaces, but clicking plus button to add new did not work. Which quickly left me with no network on my machine :-)

Some googling later and it seems to be an issue carried over from times when my machine had Leopard installed and some preferences were saved on the disk and carried over. Here is the fix:

defaults delete NSGlobalDomain NSUseLeopardWindowValues
defaults delete com.apple.Safari NSUseLeopardWindowValues
defaults delete -g AppleUseCoreUI
killall SystemUIServer