CPU mysteriously being used by nothing

"You have a load average of 2-3. That's a lot for what you think is an idle system. Try checking if you have some processes that are permanently (or almost) in state other than S (sleep):

ps auxwww | grep -v S

Also look at the output of vmstat (""vmstat 2"" for example).

With high load you either have one or more process running that uses CPU, which should show up if you sort your output from ""top"" (the default sorting is often the one you want), or it's bursty in that the load is taken by short-lived processes. Those are harder to find.

Try killing off services and see when/if the cpu use goes down. Start with shutting down X and going to console, then shut down service after service with commands like /etc/init.d/cron stop.

That gconfd in your screenshot sticks out a bit though."