Ubuntu – Wrong window gets focus when switching workspace

You could try upgrading to 12.04, there have been many improvements to the way dual screens are handled, and you can control better how the launcher works with dual screen (on System Settings > Displays, and System Settings > Appearance > Behaviour). If it still doesn't work for you can you add more detail to the question please? I am not sure exactly what you are seeing. But try it in 12.04 first.

Taken from an OP's edit:

Google Chrome's Hangouts extension had its "Keep Hangouts on top of other windows" option switched on. So you'll have to forgo pinning the Hangouts chats to the notification panel to get focus working properly again.