I'm having same the same problem since move from 10.10 to 11.04 about 3 weeks 
ago It did work OK for a while with early April version of 11.04 beta then went 
this way after an upgrade. Have re-installed twice - no luck. Though it was a 
Unity problem at first and raised a query but no response.
https://answers.launchpad.net/ubuntu/+source/unity/+question/153784

 Using Sony Laptop VGN-A617S with ATI RADEON X700.
Thought it was Unity at first but have removed that (which sometimes worked 
OK). Does not shut down properly even after 2 hours!. Have also noticed during 
startup that screen shows white vertical bars on black background for about 1 
second. During shut-down the Ubuntu screen with 5 dots does not appear. About 1 
in 10 - 1 in 20 times everything works OK just once.
Again like many others if any further info would help please let me know (but I 
need simple instructions being a novice).

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https://bugs.launchpad.net/bugs/762203

Title:
  Computer is not turned off at sutdown

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