I've had this problem with 12.04 for a while. Had no idea what caused
it. Found a fix in ubuntuforums renaming priorities in upstart scripts
but never bookmarked the thread(12.04beta)

Struggled on recent install until I noticed reboot/shutdown worked when 
dropping to tty1 and stopping lightdm service. I have updated my AMD graphics 
driver to Catalyst version 12.4 and so far everything is back to normal, 
including plymouth. 
Will see if it persist.
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Radeon HD 6700 Series ;  i7-2600 ;  H67 Express Chipset
Linux bean-desktop 3.2.0-24-generic #39-Ubuntu SMP Mon May 21 16:52:17 UTC 2012 
x86_64 x86_64 x86_64 GNU/Linux

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https://bugs.launchpad.net/bugs/987220

Title:
  System does not power off reliably when "Shut Down" chosen from GUI

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