Look at the CPU graphs under the "Performance" tab. CPU usage by normal tasks is shown as a green line. CPU usage by the kernel is shown as a red line.
Since you're saying that you've got 100% CPU usage but it's not showing up in any process, I'm guessing that you've got a graph that shows a red line?
If so, your system may be handling an excessive amount of interrupts. One possible cause of this might be a disk that's running in PIO instead of DMA mode.