Windows can go 100% CPU bound in some driver or service and not show up. In fact my favorite one are network shares that are offline and every 10 minutes the CPU gets busy.
Your post tells so little that maybe you can share more. If it is truly hidden tell us what you do to look for ROOTKITS which hide quite well.
I have a Celeron 2.5GHz, 760mb RAM running XP SP2. Now and again, my computer just grinds to a hault. Things still work, but very, very slowly. When I open task manager the performance tab reads CPU running at 100%, but when I click on Processes (and with all users checked) it read 00 in CPU column for ALL programs. Apparently nothing is running, yet the CPU is at full hilt. The only way to stop it is either wait it out and (most times) it eventually sorts itself out and returns to normal functioning or Restart. It is very annoying and shouldn't really happen.
Help, please help.