I've experienced similar behavior twice on two different Kubuntu Karmic
Alpha 3 installations (one upgraded and one clean installation). I
cannot identify what goes wrong, some application may be closed but the
logout procedure is stopped and you can continue using the desktop.
Trying logout again does nothing after that. Reproducing this bug may be
difficult, since it occurs only in rare occasions in my case.

By the way, a better way to reboot is using shutdown:

shutdown -r now

and -h options halts the machine.

-- 
Logout/Shutdown do almost nothing
https://bugs.launchpad.net/bugs/412692
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