Thank you for your bug report. I'm assigning this to gnome-terminal,
because x-terminal-emulator points to gnome-terminal by default, and I
can confirm this behaviour. When running from the terminal, I see:

ch...@chris-desktop:~$ gksu /usr/bin/x-terminal-emulator 
Failed to contact the GConf daemon; exiting.ch...@chris-desktop:~$

If you want a root terminal, open your terminal emulator and run:

sudo -s -H

** Changed in: gnome-terminal (Ubuntu)
   Importance: Undecided => Low

** Changed in: gnome-terminal (Ubuntu)
       Status: New => Confirmed

** Changed in: gnome-terminal (Ubuntu)
Sourcepackagename: None => gnome-terminal

** Tags removed: menu root system terminal tools

** Summary changed:

- Under System Tools, Root Terminal will NOT run.  It crashes. 
+ Under System Tools, Root Terminal will NOT run.

-- 
Under System Tools, Root Terminal will NOT run.  
https://bugs.launchpad.net/bugs/348573
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