Joseph,
 
This is in .xsession-errors:
/etc/gdm/Xsession: Beginning session setup...
SESSION_MANAGER=local/narwhale:@/tmp/.ICE-unix/4168,unix/narwhale:/tmp/.ICE-unix/4168
1245556817.745420 Session manager: disconnected...
Warning: program compiled against libxml 207 using older 206
Warning: program compiled against libxml 207 using older 206
Warning: program compiled against libxml 207 using older 206
Window manager warning: Failed to read saved session file /home/mark/.config/metacity/sessions/default0.ms: Failed to open file '/home/mark/.config/metacity/sessions/default0.ms': No such file or directory
Warning: program compiled against libxml 207 using older 206
Warning: program compiled against libxml 207 using older 206
Warning: program compiled against libxml 207 using older 206
Warning: program compiled against libxml 207 using older 206
GNOME_KEYRING_SOCKET=/tmp/keyring-u7nyMw/socket
SSH_AUTH_SOCK=/tmp/keyring-u7nyMw/socket.ssh
Warning: program compiled against libxml 207 using older 206
20/06/2009 09:00:31 PM Autoprobing TCP port 
20/06/2009 09:00:31 PM Autoprobing selected port 5900
20/06/2009 09:00:31 PM Advertising security type: 'TLS' (18)
20/06/2009 09:00:31 PM Advertising authentication type: 'No Authentication' (1)
20/06/2009 09:00:31 PM Advertising security type: 'No Authentication' (1)

** (nautilus:4409): WARNING **: Unable to add monitor: Not supported
nautilus: symbol lookup error: /usr/lib/librsvg-2.so.2: undefined symbol: xmlNewEntity

(nautilus:4417): Unique-DBus-WARNING **: Error while sending message: Message did not receive a reply (timeout by message bus)
Unable to open desktop file /usr/share/applications/openoffice.org2.4-writer.desktop for panel launcher: No such file or directory
Unable to open desktop file /usr/share/applications/openoffice.org2.4-calc.desktop for panel launcher: No such file or directory
Unable to open desktop file /usr/share/applications/openoffice.org2.4-base.desktop for panel launcher: No such file or directory
Warning: program compiled against libxml 207 using older 206
epiphany-browser: symbol lookup error: /usr/lib/librsvg-2.so.2: undefined symbol: xmlNewEntity
Warning: program compiled against libxml 207 using older 206
epiphany-browser: symbol lookup error: /usr/lib/librsvg-2.so.2: undefined symbol: xmlNewEntity
Warning: program compiled against libxml 207 using older 206
Warning: program compiled against libxml 207 using older 206
epiphany-browser: symbol lookup error: /usr/lib/librsvg-2.so.2: undefined symbol: xmlNewEntity
nsHeaderInfo: registerSelf called!
nsHeaderInfo: registerSelf called!

compiz was not installed for some reason, so I tried installing it, but no change.
It appears that I have two versions of libxml2 installed - 
/usr/lib/libxml2.so.2.7.3
/usr/local/lib/libxml2.so.2.6.30
but dpkg says I only have one:
narwhale:/home/mark# dpkg -l libxml2*
Desired=Unknown/Install/Remove/Purge/Hold
| Status=Not/Inst/Cfg-files/Unpacked/Failed-cfg/Half-inst/trig-aWait/Trig-pend
|/ Err?=(none)/Hold/Reinst-required/X=both-problems (Status,Err: uppercase=bad)
||/ Name Version Description
+++-=========================-=========================-==================================================================
ii libxml2 2.7.3.dfsg-1 GNOME XML library
un libxml2-dev <none> (no description available)
un libxml2-doc <none> (no description available)
un libxml2-headers <none> (no description available)
un libxml2-python2.3 <none> (no description available)
ii libxml2-utils 2.7.3.dfsg-1 XML utilities
narwhale:/home/mark# 

I remember several of those warning about libxml during apt-get upgrade. I don't know if this is the problem, but one of the errors in .xsession-errors mentions an unknown xml entry.
I don't know how to "blow away" my gconf or gnome configuration as suggested by James, nor do I understand if that will help. 
 
Any further suggestions would be greatly appreciated!
 
Mark


On Sat, Jun 20, 2009 at 7:21 PM, Joseph Sinclair <plug-discussion@stcaz.net> wrote:
From the sound of it Nautilus is not starting or failing on startup.
Have you looked at .xsession-errors?  There may be something there about a dbus failure.
Try (from a command-line if you can get a terminal started) running nautilus directly, if that "fixes" the problem, then you know for certain what's failing (you might also get debug output that can help tell you why).
If you can't start Nautilus, try disabling compiz, sometimes that causes problems during upgrades.
I had a similar problem in a stable release, and I had some luck with (via command-line) disabling compiz and dropping back to a simpler graphics driver (kernel drivers first, VESA if those fail).  You might have some luck trying that.
If all else fails, you might need to blow away your gnome configuration files (back them up first!) as suggested by James.


Mark Phillips wrote:
> I am running Debian testing on my laptop. Just completed a routine apt-get
> update apt-get upgrade, and now all my desktop icons are gone and every time
> I access the menus (Applications, Places, System) the upper and lower menu
> bars disappear and then come back. I am writing this email in a browser
> window, so once an application is launched it seems to work OK.
>
> I have no idea where to start debugging this problem. Any suggestions are
> welcome!
>
> Mark
>
> P.S. I am running gnome, not KDE. Also, I cannot right click on the desktop
> - nothing happens.
>
>
>
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