I have this problem too... Shutdown and restart don't work. But it's not fglrx 
fault, I use nvidia driver.
The 2.6.27-7-generic is working but 2.6.27-3-rt is not working. I think that is 
because of some kernel option or the specific version that has some problem.

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2.6.27-3-rt shutdown not working
https://bugs.launchpad.net/bugs/286960
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