I am having the same problem with windows in the taskbar not raising to the 
top.  This looks like a problem with the application Metacity - gnome windows 
manager.  I am running metacity 2.20.0 on
Mozilla/5.0 (X11; U; Linux i686; en-US; rv:1.8.1.12) Gecko/20080207 Ubuntu/7.10 
(gutsy) Firefox/2.0.0.12
I found a simple way to reproduce the problems in IDLE the IDE for Python.  
IDLE can be installed from
the Synaptic Package Manager, just search for IDLE the integrated development 
environment for python.

Launch IDLE, then click FILE then click NEW WINDOW, this creates UNTITLED 
within the UNTITLED window click RUN then click PYTHON SHELL
PYTHON SHELL comes to the top as the active window, as it should.

Here is where it gets screwy
Now click on UNTITLED in the taskbar, this brings UNTITLED to the top as the 
active window as it should
then click RUN then click PYTHON SHELL!!!
now for some reason the window PYTHON SHELL does NOT come to the top as the 
active window instead
it sits blinking in the taskbar as if the UNTITLED window was made to be Always 
On Top.
Now, click on PYTHON SHELL in the taskbar, it Minimizes the PYTHON SHELL 
window???
click on PYTHON SHELL in the taskbar again and it Maximizes the PYTHON SHELL 
window
raising it up to the top active window.

Now try this, make the PYTHON SHELL window the active top window and minimize 
it.
Now within the UNTITLED window click on RUN then click on PYTHON SHELL, now
it works??? the PYTHON SHELL window raises to the top active window

For some reason if the PYTHON SHELL window is minimized it works and if it is 
not minimized it does not work.
And yet when one first launches IDLE it works.

Metacity has got problems. The new 2.21 version is out but I have never
compiled so i'll wait for an Ubuntu update.

Also, setup Java and go play some free poker at Party Poker Anytime in more 
than one window.
It is absolutedly insane. One has to click on a window to activate it and then 
click on the window that
is blinking to get it to goto active top ... completely NUTZ.  When an 
appplication calls for a window to
activate,  it should raise to the top, no clicking involved.

-- 
window list should raise window
https://bugs.launchpad.net/bugs/175401
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