Huh? Your accounts are in .gconf? Mine are stored in couchdb, along with
messages and preferences:

ed...@edgar-laptop:~$ ll .local/share/desktop-couch/gwibber_*
-rw-r--r-- 1 edgar edgar  20571 2010-05-02 10:28 
.local/share/desktop-couch/gwibber_accounts.couch
-rw-r--r-- 1 edgar edgar 495716 2010-05-05 12:44 
.local/share/desktop-couch/gwibber_messages.couch
-rw-r--r-- 1 edgar edgar  69723 2010-05-04 12:15 
.local/share/desktop-couch/gwibber_preferences.couch

Mine is a fresh install of Lucid, not an upgrade. Is that what is
causing this difference, I wonder...

To remove an application and configuration files (that are installed with the 
package) you are supposed to use:
sudo apt-get purge packagename
However, I don't think that removes data that is created by the installed 
application when it is running -- so I think you'd have to manually delete the 
~/.gconf/apps/gwibber and ~/.cache/gwibber folders to get rid of its 
configuration and cached data.

To compare the couchdb installed packages and versions, could you run:
dpkg -l "*couch*" | grep '^ii'
and paste the output?

Here is what the versions are on my installation:
ii  couchdb-bin                           0.10.0-1ubuntu2                       
          RESTful document oriented database, programs
ii  desktopcouch                          0.6.4-0ubuntu3                        
          A Desktop CouchDB instance
ii  evolution-couchdb                     0.4.5-0ubuntu1                        
          Evolution support for CouchDB databases
ii  libcouchdb-glib-1.0-2                 0.6.3-0ubuntu1                        
          GLib-based API for CouchDB
ii  libdesktopcouch-glib-1.0-2            0.6.3-0ubuntu1                        
          Glib-based API for Desktopcouch
ii  python-couchdb                        0.6-1                                 
          library for working with Apache CouchDB
ii  python-desktopcouch                   0.6.4-0ubuntu3                        
          Python Desktop CouchDB
ii  python-desktopcouch-records           0.6.4-0ubuntu3                        
          Desktop CouchDB Records API

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