here's a stupid idea: add
gnome-terminal -e top
to your System>Preferences>Sessions Startup Programs. I you're lucky it'll launch a terminal with top running so you can see what process is bothering.
besides that, there *is* a log file under System>Administration>System Log. Have a look at the syslog, messages and others from the left pane. This:
Nov 29 19:25:11 desktop kernel: [ 0.000000] Linux version 2.6.24-16-generic (buildd@palmer) (gcc version 4.2.3 (Ubuntu 4.2.3-2ubuntu7)) #1 SMP Thu Apr 10 13:23:42 UTC 2008 (Ubuntu 2.6.24-16.30-generic)
is from the messages log, close to boot time. The time of the log is shown far left and the [ 0.000000] is a more accurate timer. Whatever is causing you trouble should be logged. After a fresh boot, check the log and note the differences between times. The offending process is likely to have larger difference between its log time and the previous. It will also be towards the bottom of the log. Good luck.