I have exactly the same problem. Same settings (do nothing on closing lid).
Kubuntu 13.10
Dell Inspiron 9400, latest BIOS

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https://bugs.launchpad.net/bugs/1276659

Title:
  suspending on shutdown when lid is closed

Status in “gnome-power-manager” package in Ubuntu:
  New

Bug description:
  Description of the problem:
  When power-settings are set to do nothing when lid is closed, my computer 
most of the times suspends on shutdown, only shutdown. When lid is opened the 
shutdown is continued.

  Result 9 cases out of 10:

  1. Setting options to do nothing (not suspending) on closing lid on my laptop.
  2. Open terminal and type "sudo shutdown -P 5 min"
  3. Close Lid.
  4. Wait for shutdown. 
  5. Wait for suspend.
  6. Open the lid. (You will find  the computer in suspended mode. It always 
displays its final logo before shutdown when opened. So actually the shutdown 
is triggered and in progress, but is then interrupted by a suspend instruction.)
  7. The computer continues to shutdown, when lid is opened.

  Expected result:

  1. Setting options to do nothing (not suspending) on closing lid on my laptop.
  2. Open terminal and type "sudo shutdown -P 5 min"
  3. Close Lid.
  4. Wait for shutdown. 
  5. The computer is off.

  When I don't close the lid everything goes as expected.

  I actually have a backup script running when I shutdown the computer
  and the last thing it does is to shutdown the computer.

  I have run Debian with gtk 2 successfully. I have run Ubuntu
  successfully before Unity. Now I run UbuntuGnome.

  I think there is a change in option, set to the kernel during
  shutdown, which triggers the suspend.

  A page (https://wiki.ubuntu.com/Bugs/FindRightPackage) suggests gnome-
  power-manager, pm-utils, or the kernel to be the failure.

  patrik@Ubuntu:~$ lsb_release -rd
  Description:  Ubuntu 13.10
  Release:      13.10

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