Since I've had to install a new version on November 1st, I've seen this happen. It doesn't happen allways, but sometimes. But I've seen it happen on two different computers. (One a standard 32 bit Windows XP home edition and a Windows XPx64 professional machine)

At startup, at first the icons appear cluttered. As usual. Then when fences has started they're moved into their ...ehm... fences. Still as before. But...
Some icons are not shown completely. Some are randomly missing a quarter or a left or right half. Some don't even show up at all. On the other hand, when I had my icons hidden when I switched my computer off last time, they will be hidden at startup. But then it turns out a few icons are partially shown.

The workaround is to doubleclick the desktop twice, thus showing and re-hiding the icons (or the other way around). Then it's okay. It's just that it doesn't go well at startup. I've never had this before in previous versions.

Hope you'll find a solution.

P.S. Thanks for fixing the bug where two program files folders showed up after locking the computer using ctrl-alt-del.