12.04 - system slows down from time to time, reason unknown

Hi,

My system:
12.04 64 bit (clean install after stable release)
Kernel: 3.2.0-24-generic
3,7 GB RAM
i3 M330 @ 2.13GHz CPU
(HP ProBook 4320s)
at least 60% free space on every partition

The problem:
The system slows down from time to time for no apparent reason.

Slows down: e.g. it takes 30 secs to open a folder in Nautilus. System monitor and top in terminal show high or well over average CPU usage values for everything, even above 100%...

From time to time: about once every 4 hours on average , but it is absolutely unpredictable. I may use the laptop for a day without any problem or get this issue only after a few minutes.

No reason: I had three suspects after some googling, system updater, Firefox and Compiz. Switched off auto updates and switched to chrome but no luck there... Compiz did not show over average CPU usage in some instances, so I dropped that possibility too.
I used top in terminal to monitor what happens and killed everything I could, but no result. I tried iotop but nothing suspicious.

After logging out the problem remains, that is, even the login screen responses very slow. Tried killing x with ctrl+alt+backspace, still slow. (restarting works, hurray). Once or twice I have been patient enough to experience that after a while (10 minutes?) the system turns back to normal speed.

One more thing: I experienced the problem with my 11.10 install too, but not from the beginning (maybe from January?)

So, any thoughts how to proceed?

Thank in advance.
Istvan