I have the same problem.

I am running ubuntu 10.04 LTS with all updates.

Description:
The problem occurs when having a vertical taskbar. Once you have more than a 
certain number of windows open (determined by resolution and the pixel size 
used in the properties for the taskbar), the taskbar will add another column 
(see attached picture).

Then when you try to click on a window icon - it moves back into one
column, and mostly the window does not move into focus as it usually
will.

It looks like the taskbar thinks the first column is full, and then adds
another, most likely a problem with the way the size of the icons is
calculated. Perhaps it is using the length of the icons instead of the
height to determine if the one column is full - this would be the case
with a horizontal taskbar.

The real problem is not the two colums, but the fact that on the first
click the icons will return to one column, without activating the
selected window, if you are fast you can then click the icon when in one
column and activate it.

Basicaly this behavior handicaps the vertical taskbar beyond use if you
like to have many open windows.



** Attachment added: "tasbar.jpg"
   
https://bugs.launchpad.net/ubuntu/+bug/463644/+attachment/1737132/+files/tasbar.jpg

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strange behaviour of vertical gnome taskbar with 7+ applications
https://bugs.launchpad.net/bugs/463644
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