I also have this bug. 
I use KAlarm and my computer with Ubuntu 12.04 (Gnome desktop) took several 
minutes to shutdown.

Link http://ubuntuforums.org/showthread.php?t=1764048 gave me the hint how to 
solve this problem. This link contains methods to prevent te starting up of 
nepomuk and akonadi in 3 steps. 
If you don't want to use KAlarm, it might be safe to apply all three steps. 
However, doing so, KAlarm could not be used. It asked to start-up akonadi 
first. So I tried what would happen if I only used the two steps preventing the 
(complete) start-up of nepomuk, and that worked great. KAlarm works and Ubuntu 
12.04 shuts down within a few seconds. The steps to apply are:

1. Add the following lines to ~/.kde/share/config/nepomukserverrc (and
their sections if they don't exist) (change the value from "true" to
"false" if they do exist and are set on "true";

[Basic Settings]
Start Nepomuk=false

[Service-nepomukmigration1]
autostart=false

[Service-nepomukstrigiservice]
autostart=false

2. Remove the file /usr/share/autostart/nepomukcontroller.desktop, if it
exists.

-- 
You received this bug notification because you are a member of Desktop
Packages, which is subscribed to gnome-session in Ubuntu.
https://bugs.launchpad.net/bugs/1053783

Title:
  Ubuntu 12.04 - Stalled shutdown after having had KAlarm opened; with
  package info.

Status in “gnome-session” package in Ubuntu:
  Confirmed

Bug description:
  In Ubuntu 12.04, the shutdown is stalling - for about 2 minutes - but only on 
occasions when I have opened - and then quit - KAlarm. 
  A window pops up Stating that, 'A Program is still running'; Unknown (not 
responding); and, there are 3 buttons to choose: 'Lock Screen', 'Cancel' and 
'Shutdown Anyway'.

  Initial report was Bug #1053779 but had no package information.

  ProblemType: Bug
  DistroRelease: Ubuntu 12.04
  Package: gnome-session-bin 3.2.1-0ubuntu8
  ProcVersionSignature: Ubuntu 3.2.0-30.48-generic-pae 3.2.27
  Uname: Linux 3.2.0-30-generic-pae i686
  NonfreeKernelModules: nvidia
  ApportVersion: 2.0.1-0ubuntu13
  Architecture: i386
  Date: Fri Sep 21 13:22:35 2012
  ExecutablePath: /usr/bin/gnome-session
  InstallationMedia: Ubuntu 12.04 LTS "Precise Pangolin" - Release i386 
(20120423)
  ProcEnviron:
   LANGUAGE=en_AU:en
   PATH=(custom, no user)
   LANG=en_AU.UTF-8
   SHELL=/bin/bash
  SourcePackage: gnome-session
  UpgradeStatus: No upgrade log present (probably fresh install)

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