While I haven't entirely reached the bottom of this problem my colleague has identified a workaround:
When someone logs out of a GNOME session, it tries to read the ~/.gnome2/xsession file. If this file is not populated (just the presence of an empty file with this name is NOT enough), then the session will stall for 2-3 minutes on logout. (Curiously, killing X at this stage also kills gdm. This doesn't happen at any other time.)
If you click "Save session" in the logout dialogue, the session will still freeze, but it will be the last time. All subsequent login/logouts go without a hitch. It is this process that creates and populates the ~/.gnome2/xsession file.
Unfortunately this means that for every user, they are guaranteed at least one stalled logout. I tried putting a template in /etc/skel, but the file has many references to absolute home directory paths (eg /root), and it doesn't seem to parse the "~" ("current user home directory") character.
This strongly points to a bug in GNOME.
Greg
