The problem still exists on 12.04 beta2.
As a work around, on Unity, one could go to CompizConfig Settings Manager->General Options->Focus & Raise Behaviour, and make Focus Prevention Windows box look like: "!(class=Polkit-gnome-authentication-agent-1) & !(class=Transmission-gtk)"
The problem still exists on 12.04 beta2. Polkit- gnome-authentic ation-agent- 1) & !(class= Transmission- gtk)"
As a work around, on Unity, one could go to CompizConfig Settings Manager->General Options->Focus & Raise Behaviour, and make Focus Prevention Windows box look like: "!(class=