After updating to Snow Leopard 10.6.8 (from leopard 10.5) and the restoration of configurations and saved files, I can't no longer turn off my iMac normally.
The shutdown option is restarting the iMac.
Click on the Disk Utility located in Applications > Utilities > SOS tab.
Select your primary drive and click "repair permissions".
You can also make use of a small utility to fix this issue.