Hi,
While attempting to reproduce this problem for someone else at 
ubuntuforums.org, I found myself "stuck" with the same problem too in Ubuntu 
10.10. While in a "Ubuntu Desktop" session "metacity --replace" and "sudo 
update-alternatives --config x-window-manager" did not help at all. The results 
were always the same, Ubuntu Desktop session always had the e16 window manager 
running instead of metacity. Ever since trying out an e16-gnome session, I was 
also having trouble with "indicator-appmenu" from my "Ubuntu Netbook" session 
which was covering my main menus in my "Ubuntu Desktop" session. We both had 
ubuntu-desktop, ubuntu-netbook and e16 desktops installed. I offered the e16 
removal advice as follows, which works well for me. 

Remove e16 and its dependencies:
$ sudo apt-get remove e16
$ sudo apt-get autoremove
Now if you don't have any window borders, try this:
$ sudo update-alternatives --config x-window-manager
(choose metacity)
Now restart, or log out and log back in.

---Part 2---
If you still don't have any window borders for your applications, try this:
$ metacity --replace
Your window borders should appear correctly now. 
If that works, go to System > Preferences > Startup Applications and create a 
new entry for metacity --replace.
> Name = Metacity  
> Command = metacity --replace
Now restart your computer and see if that Startup Application entry works. This 
will be only a temporary solution.

---Part 3---
IF (only if), you have a problem with indicator-appmenu like I am (it is like a 
global menu) automatically appearing on your panel of your "Ubuntu Desktop" 
session, and covering your menus, try this:
$ sudo apt-get remove indicator-appmenu
$ sudo apt-get autoremove
Now restart, or log out and log in and the appmenu problem should be gone.

This solution works well for me, and I have successfully restarted a 'normal' 
Ubuntu Desktop session about 10 times already.
Ubuntu forums post for anyone interested: 
http://ubuntuforums.org/showthread.php?t=1593463
Thanks.

-- 
Launching alternate Window Manager changes default Window Manager with no 
option to reset
https://bugs.launchpad.net/bugs/616763
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