If system settings is in the background, and you select it from the system drop down, the icon on the unity launcher will give an indication but it will not open unless no selection has been made from the "all settings" overview window. It only give this indication once; subsequent selections give no further indication on the Launcher. Interestingly, if you open systems settings overview but make no further selection before putting it in the background the systems settings will always open.
The fact that this behaviour changes after a further selection is made might be considered a bug though I can't find a bug report matching this description.
To some extent I skipped this bug entirely because I have system settings locked to the launcher and access it that way. This always works, even if one of the sub-windows is open (the sub-window is closed and the overview window opens).