I have an odd issue when trying to shutdown or restart using the shutdown applet. When shutting down or rebooting it acts as if it is going to return to the gdm login window. I have an Nvidia card, that has a highspeed fan. So I know when the drivers are kicked in or not, because the fan speed reduces when X starts. So when I use the applet it causes the fan speed to go high back to low then back to highspeed, then it proceeds to shutdown. Very odd

I can see that it is trying to restart X, then proceeds to shutdown. This all makes a mess of my splash, because it tries to reset X and my shutdown splash works sometimes, or I get a INIT shutdown message with a blinking cursor until shutdown or reboot. I do not have these issues if I use the command prompt.

I don't know where to begin to start a diag of this issue. I have checked logs etc. And I do not see anything that warrants an alarm.

You should post this problem on your distributions forums since you haven't even posted your distribution details, let alone versions for Gnome, kernel, etc.