First of all, this is _not_ a bug within compiz, I am using metacity. You can 
indeed reproduce the bug with the default ubuntu 9.04 iso _without 
modifications_ to it. Just burn the standard cd, boot it, fire up ubuntu. Once 
your logged in, press alt+f2, enter firefox. hit enter. Firefox will be started 
within a window which has the title "Welcome to Ubuntu 9.04 - Mozilla Firefox". 
Then right-click onto that exact place, the top bar colored in orange. In the 
context menu, check "Always on top". If you now hit alt+f2 again, the "run 
application" dialog will _not_ get focus( its titlebar stays white). This 
happens even if you minimize firefox. This is in my opinion definitely a 
papercut, because users would expect to be able to enter a command in a  "run 
application" window without clicking it to get it focused first.
Concerning Karmic: Afaik there are so far only release candidates of this 
ubuntu version. I am however a user and not an active developer. Thus I am not 
using release candidates.

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New windows don't get focus when other window is "always on top"
https://bugs.launchpad.net/bugs/392241
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