Well that was pretty scary. It consistently showed the problem after about 10 different restarts, so I figured it wasn't going to fix itself anytime soon.
Now I know practically nothing about linux, but making the copy of the fglrx.ko seemed to cause a problem. And when I reinstalled the new modules it was still there. So I decided to run
and then reinstall the modules once more.Code:sudo rm /lib/modules/`uname -r`/misc/fglrx.ko
After restarting back into Gnome again the problem was still there and my windows were acting funky. So I booted into Fail Safe Gnome and the CPU problem disappeared. Next I tried booting into XGL and the problem wasn't there. Finally I booted into regular Gnome again and it disappeared this time. Weird. I'll post back when I understand this more.
Well it looks like I was very wrong. Restarting into either Gnome or XGL still gives me the error. It only works when I first log into Fail-Safe Gnome. That's when I get an error about the gnome-settings-daemon which I have set to automatically run at login. This daemon is probably whats using all the CPU up and not showing any trace at all. This seems to be a big problem that several people have...and I still don't know of a solution. I'm going to keep messing around with my settings until I catch a break.