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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https://bugs.launchpad.net/bugs/1053783

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

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