With Ubuntu 9.10 Karmic Koala, there is a 60 second confirmation delay when logging out, restarting or shutting down. This default can be over-ridden to act instantly rather than waiting for a confirmation (and 60 second timeout) by setting the apps/indicator-session/suppress_logout_restart_shutdown boolean to true as follows:
gconftool-2 -s '/apps/indicator-session /suppress_logout_restart_shutdown' --type bool true
(or use gconf-editor to do this if you want to use a GUI based tool).
I suspect the rationale behind the 60 second confirmation delay is just in case one selects logout, restart or shutdown accidentally and in doing so, one has the ability to cancel this before accidentally closing one's session. So beware if you use this tweak - it assumes you really want to instantly logout, restart or shutdown!