As I unterstand, unchecking the "Prompt on logout" under Settings -> Session and start up -> General should avoid the "wait 30 seconds..." prompt when logging out (as well as shuting down the system, etc.). Unfortunately it doesn't. BTW. I'm using a fresh install of Xubuntu 12.04 and the only setting so far concerning session management I've done, is "starting gnome services on start up".
This 30s dialog is provided by the Actions plugin of xfce4-apnel which indeed does not read this setting. I'm assigning the bug to the correct component.
Closing old bugs