Thanks for the bug report. I'd like to help, so I followed your suggestions and opened a root VT.
My desktop is running FC 16 in a server configuration (apache, etc.), used for development. There are a LOT of processes running. I tried your suggestion and found that
were running after logout. When I killed all the processes, it hosed the XFCE window and I had to reboot. In hindsight, this makes sense.
To get some insight, I did a clean boot and removed .x-sessions-error to get a clean log. I captured the running processes up to the XFCE login window.
x-proc-B4-login.txt - all processes running up to the XFCE login window.
After login, I got the corrupted symptoms - the desktop icons appeared before the taskbar. (The window borders are now corrupted.)
xsession-errors-afterlogin.txt - errors after login, nautilus-gdu is shutdown
xsession-errors-before.txt - I forget when I captured this.
.xsession-errors.txt - the last file I captured.
My guess: I think a process is starting out of sync with something and the errors are cascading until nautilus finally gives up. It then attempts to restart and it's probably too late. The only way to fix this is to wait for a signal to start. Which signal to what process, I don't know.
(tracker-store:1946): Tracker-CRITICAL **: D-Bus service name:'org.freedesktop.Tracker1' is already taken, perhaps the daemon is already running?
Shutting down nautilus-gdu extension
Initializing nautilus-gdu extension
(nautilus:2356): libnotify-WARNING **: Failed to connect to proxy
Do you need any more information? Should this be filed with the bug report?