I have exactly the same problem. In fact it gets worse. If I force the
shut down I find that on restart a full file system check is forced and
I am getting file system corruption!!!

My workaround is to log off before I shutdown. I log off and get a
message that an unknown program is running and I force the logoff. Then
I shut down. This seems to avoid the problem of file system corruption.
However it means that shutdown has an annoying 2 minute wait (for the
program to be terminated during logon) then I have to shut down.

Another workaround is to press the restart button on the computer. If I
do this there is no annoying 2 minute wait and no file system
corruption. It amazes me that hitting the red button is less problematic
than doing an orderly shutdown.

So there are several problems here

1. I run kalarm and terminate it correctly. This results in a problem shutting 
the system down and at best a 2 minute delay. Problem #1.
2. The name of the offending program that is delaying the shutdown is not 
displayed. You only get "unknown". Problem number 
#2. 
3. There is a 2 minute delay after you choose to force termination of the 
program. Problem #3
4. File system check forced on restart. Problem #4.
5. File system corruption detected on restart. Problem #5.

This is the flakiest linux install since Slackware with Linux 0.99 which
was flaky mainly due to the X driver.

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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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