This problem can be solved with by adding 1 line of code to window-
list.c within the gnome-panel source.

First ensure you have the latest versions of gnome-panel and libwnck22.

dpkg -l gnome-panel libwnck22
ii  gnome-panel                  1:2.30.2-1ubuntu3            launcher and 
docking facility for GNOME
ii  libwnck22                    1:2.30.5-0ubuntu1            Window Navigator 
Construction Kit - runtime files

Then get the source and build dependencies

apt-get source gnome-panel
apt-get build-dep gnome-panel

Edit applets/wncklet/window-list.c in your favourite editor and add this
line of code to the beginning of function tasklist_update, just before
the if statement.

wnck_tasklist_set_orientation(tasklist->tasklist,
tasklist->orientation);

Build the package with dpkg-buildpackage, and install the .deb file for 
gnome-panel.
Alternatively, use the attached patch file instead of manually editing the 
source code.
Restart the task list applet using;
killall wnck-applet

I hope this helps.
-- 
Craig Shelley

** Patch added: "Fix Task List Orientation Vertical Flicker"
   
https://bugs.launchpad.net/ubuntu/+source/gnome-panel/+bug/43066/+attachment/1790741/+files/tasklist-orientation-fix.patch

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Desktop Bugs, which is a direct subscriber.
https://bugs.launchpad.net/bugs/43066

Title:
  Window list behaves bad when panel is vertical.

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