There seems to be a problem with startup notifications in nautilus in that it doesn't notify about startup completion.

I've enabled debugging in Metacity by setting METACITY_VERBOSE=1 and METACITY_USE_LOGFILE=1 environment variables. Metacity reports nautilus startup events as follows:

STARTUP: Received startup initiated for unity-2d-shell-3355-pawel-VirtualBox-nautilus-0_TIME474198 wmclass (unset)
...
STARTUP: Sequence used 6174.63 seconds vs. 15000 max: unity-2d-shell-3355-pawel-VirtualBox-nautilus-2_TIME483035
STARTUP: Sequence used 15011.9 seconds vs. 15000 max: unity-2d-shell-3355-pawel-VirtualBox-nautilus-0_TIME474198
STARTUP: Timed out sequence unity-2d-shell-3355-pawel-VirtualBox-nautilus-0_TIME474198
STARTUP: Received startup completed for unity-2d-shell-3355-pawel-VirtualBox-nautilus-0_TIME474198

Take note of the timeout. The 'Received startup completed..' following it is just fallback code in metacity, as startup complection event is actually never reported by nautilus.

Just for reference, here is how it looks for firefox:

STARTUP: Received startup initiated for unity-2d-shell-3355-pawel-VirtualBox-firefox-1_TIME476779 wmclass (unset)
STARTUP: Adding sequence unity-2d-shell-3355-pawel-VirtualBox-firefox-1_TIME476779
STARTUP: Sequence used 421.761 seconds vs. 15000 max: unity-2d-shell-3355-pawel-VirtualBox-firefox-1_TIME476779
STARTUP: Received startup completed for unity-2d-shell-3355-pawel-VirtualBox-firefox-1_TIME476779

I've also traced xevents with 'xev -root'. When nautilus is started it send _NET_STARTUP_INFO_BEGIN event, followed by a number of _NET_STARTUP_INFO events. This is different than startup notifications for other applications - if you compare it with xevents sent by e.g. firefox or gnome-terminal, they send _NET_STARTUP_INFO_BEGIN + a number of _NET_STARTUP_INFO events, and then _NET_STARTUP_INFO_BEGIN and _NET_STARTUP_INFO events are sent again. I'm however not sure if this means anything for this issue.