Here is a strange workaround I found.  Perhaps this information can help
in debugging the root cause of this issue.

It seems that for Compiz to render the logout dialog window decoration
correctly, the "out-of-the-box" effects must be enabled.  But the new
font must be set *after* this has been done and *after* you have started
Compiz (using your startup script).


WORKAROUND...

You probably have a startup script that starts Compiz (and Emerald) when 
Kubuntu boots up.
My file is called startcompiz.sh and is located in the  folder with the 
following contents, for reference:
compiz.real --replace --sm-disable --ignore-desktop-hints ccp 
--indirect-rendering &
emerald --replace &

1. Move ~/.kde/env/startcompiz.sh to a safe location (like your Desktop).
2. Shutdown and restart your computer.
   - Your computer will bootup without Compiz.
3. From System Settings...
   a. Click Appearance
   b. Click Fonts
   c. Click Adjust All Fonts...
   d. Select the Font checkbox
   e. Select DeJaVu Sans
   f. Click OK
   g. Click Apply
   h. Click Overview to return to the main System Settings screen
3. Shutdown and restart your computer.
4. From System Settings...
   a. Click Desktop
   b. Click Enable desktop effects

   Note: steps c - g are not necessary, but I did it for good measure... 
   c. Uncheck Improved window management
   d. Uncheck Shadows
   e. Uncheck Various animations
   f. Click Screen Edges tab, and set everything to No Effect
   g. Click All Effects tab, and uncheck everything

   h. Click Apply
5. Move startcompiz.sh from the safe location back to ~/.kde/env/  .
6. Shutdown and restart your computer.
   - When you reboot, Compiz and Emerald will be enabled.
7. From System Settings...
   a. Click Appearance
   b. Click Fonts
   c. Click Adjust All Fonts...
   d. Select the Font checkbox
   e. Select your desired font (Liberation Sans, in my case).
   f. Click OK
   g. Click Apply
8. Verify that the Logout / Restart / Shutdown dialog look normal...
   a. Click K
   b. Select Leave
   c. Select Shutdown

Results:
1. The Shutdown dialog should have your selected font (Liberation Sans, for 
example) and should not have any missing window edge decoration.
2. The Window Manager should be Compiz.
3. The Window Decorator should be Emerald.

For reference, here are my system specs...
Description: Kubuntu 9.04 x64
Codename: jaunty
CPU: Intel(R) Core(TM)2 Duo CPU T7700 @ 2.40GHz x64
GPU: Intel Corporation Mobile GM965/GL960 Integrated Graphics Controller (rev 
03)

-- 
Shutdown / Logout Dialog has missing sides and corners using Compiz
https://bugs.launchpad.net/bugs/368987
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