Both CPU running almost 100% on Ubuntu

My computer has a duel core processor. I am using Ubuntu 10.10. I have a 1 GB RAM. I allocate 2 GB space for swap partition (actually 1 GB is sufficient, but I select 2GB for testing, and I am continuing with this huge space). Normally both of my CPU uses very low process. But for some days (I guess after updating 200 line kernel it occur) I am facing an uncommon problem. I found on system monitor applet and conky that, both of my CPU running about 100%. I am not sure why this happening, but feeling afraid.

I did not run any application when took the pictures below except Firefox:

Look at the image above. CPU 1 working 90.7 % and CPU 2 running 88.1%

Look at the image above closely (click to enlarge). In this list of running processes three unnamed application running at first. Ther are not like to show them, so scrollbar goes down after them automatically.

Conky also showing quite same result. CPU1 taking 89% of whole process and CPU2 also taking 89 % of system process.

When I going to shutdown my system, then this dialogue box appear. It is telling that "An Unknown program is still running". So, my ubuntu machine stop shutting down. I have to press "Shut Down Anyway" button.

I don't know why this happen to my Ubuntu 10.10 system. I upgraded 200 lines of kernel patch upgrade with a script. Is my problem casing by it? I applied recent update from ubuntu upgrade. I upgrade Ubuntu systems kernel to 2.6.35.23-generic. But problem exist as same.