Another thing which can do it - I only notice this on my main gaming machine - is if I am in some app with different full screen res (eg Half Life 2 which I take down to 1400 by 900 res for extra speed) and I pop out to another app to answer email or something all the icons outside that 1400 by 900 window get pushed up to the top left. In no particular order.

It is a PITA so I am going to grab that reskit app Tony mentioned!