Hey there,

I actually USED to have the same problem and can say for certain that the "command execution widgets" were the culprit for me. I used to have to do the "killall hildon-home" command, several times a day until I finally removed the command execution widget.
The only way I was able to single out that widget is because I had never used it before until after about a week or so into the pr1.2 update. Everything was fine until I tried using that widget to see actual battery level. It was fine before I installed it, then for the few days I had it installed my desktop would freeze at random times all throughout the day and night until I did killall hildon-home... then everything went back to normal as soon as I uninstalled the command execution widget and I havent had any problems since. My suggestion is to uninstall it and see if your problems persist, although I have a felling everything will be fine once you do. I hope this helps.