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%.  The individual processes do not add up to 100%.  I try killing lots of processes, but the overall usage continues to be 100%.  How can I find out what's hogging the CPU?
This is an unusual situation on a computer I use daily, which is never anywhere near 100% CPU unless 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.  There is no reason the processor should 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 every process, one at a time, until the problem went away, and killing vino-server finally fixed it, even though that process never went above 5%.  I had enabled Remote Desktop a few days ago (and have obviously now disabled it).
But the question remains: How did a single process manage to use 100% CPU while top only showed that process at 5%?  How do I identify culprits like this in the future?
Looks like I'm not the only one who's had this problem:
  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.