Ubuntu's System Monitor applet shows 100% CPU usage continuously. If I click it, the resources tab shows it at 100% continuously, too. If I go to processes, though, to find out which process is the culprit, there is nothing above 10%. If I run top there is nothing above 10%. I try killing lots of things, but it continues at 100%. How can I find out what's hogging the CPU?

This is an unusual situation on a computer I use daily, that normally only hits 100% CPU when I'm doing something that requires it (like loading 32 Firefox tabs) after which it goes back to a normal idle level. It's not a new install or anything. It shouldn't be maxed out. I'm not sure when it started or if I changed something that caused it to happen.

Normally I would use top or System Monitor and find the process that had gone out of control, but I can't find anything with those tools this time. It persists after reboots and everything.

And the processor is obviously hot, so it's not an erroneous reading.

Update: I tried killing any process I saw active again, and killing vino-server finally fixed the problem, even though it never went above 5%. I had enabled Remote Desktop a few days ago (and have obviously now disabled it).

How did it manage to use 100% CPU while top only showed it as 5% or so? How do I identify the culprit in the future?

Looks like I'm not the only one:

Still a problem in both jaunty & karmic. Interestingly, both System Monitor & htop do not show the sum of individual processes being anywhere near 100% cpu.