Comment 10 for bug 743588

I'm not sure if this is part of the same bug, but it appears to be a related behavior. In addition to maintaining the focus of a closed application, when applications are opened from the Unity launcher/panel thingie (sorry I don't know it's exact name, it's the panel like interface with the trashcan you can't get rid of) the previous app will retain focus, but the new window will rise to the top.

Essentially, the window for the new application will take focus, but the appmenu in the panel retains the old applications menus. Compiz/Unity appears to think that the old application has the window focus, as clicking on it's icon will not bring it back. To get the window back to the front you need to click on any other open application, then back to the one you were working on.

Steps to reproduce:

1 - Open any application (I used firefox, and chrome when I tested it)
2- Open nearly any other application (notably it doesn't appear to happen with gnome-terminal, nautilus or tilda, but it happens consistently with firefox, chrome, claws-mail, and mypaint).

Hope this helps :)