I have the same/similar problem. Possibly related to
https://bugs.launchpad.net/ubuntu/+source/gnome-do/+bug/450852 as well.

The symptom is that gnome-do is running but it's running at 200% CPU and
lookups do not work, e.g. if I type "firefox" it stays in raw text mode
and does not launch firefox. Killing and restarting gnome-do solves the
problem.

I have both Start Gnome-do at login and hide window enabled.

Some outputs:

Top:
  PID USER      PR  NI  VIRT  RES  SHR S %CPU %MEM    TIME+  COMMAND            
 2536 rala      20   0  344m  35m  18m S  198  0.9  18:48.25 gnome-do 

$ which gnome-do
/usr/bin/gnome-do

$ lsb_release -rd
Description:    Ubuntu 9.10
Release:        9.10

$ apt-cache policy gnome-do
gnome-do:
  Installed: 0.8.2+dfsg-1
  Candidate: 0.8.2+dfsg-1
  Version table:
 *** 0.8.2+dfsg-1 0
        500 http://ftp.df.lth.se karmic/universe Packages
        100 /var/lib/dpkg/status

The aforementioned kill command that Chris instructed does not kill
gnome-do successfully (sudo does not help):

r...@salporin:~$ ps -ef|grep nome-do
rala      2524  2383  0 09:25 ?        00:00:00 /bin/sh /usr/bin/gnome-do
rala      2536  2524 99 09:25 ?        00:36:13 /usr/bin/cli 
/usr/lib/gnome-do/Do.exe
rala      3646  3455  0 09:44 pts/0    00:00:00 grep nome-do
r...@salporin:~$ kill -SIGQUIT 2536
r...@salporin:~$ ps -ef|grep gnome-do
rala      2524  2383  0 09:25 ?        00:00:00 /bin/sh /usr/bin/gnome-do
rala      2536  2524 99 09:25 ?        00:38:07 /usr/bin/cli 
/usr/lib/gnome-do/Do.exe
rala      3649  3455  0 09:45 pts/0    00:00:00 grep gnome-do
r...@salporin:~$ kill -SIGQUIT 2524
r...@salporin:~$ ps -ef|grep gnome-do
rala      2536     1 99 09:25 ?        00:38:41 /usr/bin/cli 
/usr/lib/gnome-do/Do.exe
rala      3651  3455  0 09:45 pts/0    00:00:00 grep gnome-do
r...@salporin:~$ kill -SIGQUIT 2536
r...@salporin:~$ ps -ef|grep gnome-do
rala      2536     1 99 09:25 ?        00:44:11 /usr/bin/cli 
/usr/lib/gnome-do/Do.exe
rala      3756  3455  0 09:48 pts/0    00:00:00 grep gnome-do

A normal kill does do the trick however.

Just a wild guess (I have no developer knowledge of either Gnome or
gnome-do) but could this be a conflict between gnome-do's start at login
and Gnome's session recovery?

** Attachment added: "xsession-errors-pre"
   http://launchpadlibrarian.net/37915739/xsession-errors-pre

-- 
Gnome-Do fails to launch fully on gnome login
https://bugs.launchpad.net/bugs/284254
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