I have the same problem on my home build desktop computer running 64-bit Ubuntu 
12.04 with kernel 3.2.0-24. 
I have two video cards and therefore my case might be of interest for you. One 
is Nvidia GeForce 9600 GT and the other is ATI Radeon HD 4870. Soon after 12.04 
LTS was released I installed with ATI Radeon card installed. Also soon after 
that I started to experience the bug described here. 
I was testing several of these mainline kernels but I as I was player around 
with the new Ubuntu I soon turned the system unbootable. After that I installed 
Ubuntu onto a new hard drive and as I opened the case I decided to test whether 
that Nvidia card works and it did (though there was still problem with desktop 
effects but I think it claimed to be in 3D as then certain MyUnity options 
become available). I could shut down my computer and after few weeks I was 
already hoping that the bug had been crushed but when I put back in my ATI card 
the bug was back. 

I have tested 3.4.0-030400rc6 mainline kernel for a week or so and I can
shut down the computer put now ATI driver has new tricks. When I try to
install it with jockey it gives error message. When I restart Ubuntu the
driver seems to have been installed and the AMD Catalyst Control Centre
is there but it crashes when I try to use. And the Ubuntu seems to be in
2D. The same is when I use 3.2.0-24 without ATI driver. But in both
cases I can shut down the computer properly.

I can upload more logs or terminal outputs and give more information
about the hardware if needed. I just didn't want to flood the post with
information that might be irrelevant for you. I could also install
another Ubuntu onto a spare hard drive for testing purposes but that can
not happen before 7 June as I need to get some important work done and I
also need to travel. But hopefully I can still be of help somehow.

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https://bugs.launchpad.net/bugs/991977

Title:
  Ubuntu 12.04 hangs on shutdown

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