I just built a quiet system and to test the temperature I wrote a script to write the date/time, M/B and CPU temperatures from sensors to a log and called it every minute via cron:
the script /root/testtemp:
date >> /root/temp.log
sensors | grep Temp >> /root/temp.log
01 * * * * root run-parts /etc/cron.hourly
02 4 * * * root run-parts /etc/cron.daily
22 4 * * 0 root run-parts /etc/cron.weekly
42 4 1 * * root run-parts /etc/cron.monthly
* * * * * root /root/testtemp
Once this is setup, run cpuburn-in for a few hours.
What CPU is it BTW? Some do run that hot (or hotter e.g. AMD XP).
I suspect that thermal paste is the cause, at least it was for me with my old XP 2600 (now have Sempron 64 3000 which is a lot cooler). Remove all the current paste with ArctiClean and reapply some arctic silver or something. You really do not need much.
Also, what kernal are you running? 2.6.15-1.1830_FC4 Caused my PC to do a similar thing when I had my external HDD plugged in. 2.6.15-1.1831_FC4 fixed it.