When starting thunar-settings from the menu, I get an extra "Starting File Manager..." task bar entry for some 10 seconds, then this goes away (this is the entry from libstartupnotification). Apparently what happens is that thunar-settings's DBus message to Thunar --daemon somehow causes the startup notification to be re-launched. This happens both when Thunar gets DBus activated and also when it's already running. A quick workaround is to disable the StartupNotify=true in thunar-settings.desktop. I can replicate this both under XFCE and under GNOME (with gnome-panel), as well as under the Ubuntu netbook launcher. It seems to be a problem with using libstartupnotification, not a particular problem with gnome/xfce-panel.
Hmm, Thunar does not seem to use libstartup-notification at all, except for the UCA editor. So libstartup-notification would expect a window from the same process to be spawned, but this obviously isn't the case here, since thunar-settings merely sends out a DBus call. So perhaps dropping StartupNotify is not just a hack, bug the right thing to do, unless Thunar starts using libstartup-notification for its special case? Also see http://mail.gnome.org/archives/desktop-devel-list/2002-November/msg00638.html (not sure how relevant it still is, though).
This should be fixed in master. Thunar's D-Bus call now have startup notification support by means of an additional startup_id parameter. thunar-settings passes $DESKTOP_STARTUP_ID to the D-Bus call, so this should work now. Please re-open if this bug is still valid.