Had the same problem and after some reading and fiddling I looked into /etc/rc0.d and compared it with the same folder in a parallel install which has no probs with shutdown. The file /etc/rc0.d/S90halt which is linked against script /etc/init.d/halt was gone, I don't know why.
rc0.d is the runlevel seponsible for a clean shutdown and contains links to all for this shutdown process necessary scripts which are located in /etc/init.d.
I fixed this and everything is fine.
If 'S90halt' is missing in your /etc/rc0.d do the following:
Code:
sudo nautilus /etc/init.d
right click the script named 'halt', create a link, cut and paste this into rc0.d, rename it to S90halt.
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