Have you tried replacing the SD card with a fresh one with a fresh install and checking if this still occurs? I've had a somewhat similar problem and it turned out to be a dying SD card.
I will try that. At first I would like to see if I can find the problem. I would have thought that when the SD card is not responding, it would show up as "wa" in top and "%util" in iostat -x. But both are zero for the next output after a freeze.