I have some lag when i turn off icons from desktop. When I logging i have no wallpaper on background. Instead of wallpaper i have freezed logging screen. And the unity (or maybe compiz) freezes for a while time. When I turn on icons on desktop all become normal.
Yea I also have this problem, not sure what has caused it but I'll try to find some explanation. You're not alone!
Ok well, do you happen to have nitrogen installed to manage your backgrounds (such as if you wanted a wallpaper for dual screens?) In any case I was using nitrogen and it seems the desktop would freeze because I needed to initialize nitrogen and reset the wallpaper. Basically I just opened terminal and entered $nitrogen & and it worked. I'll go test it some more.
Final Edit: I just tested this and it works even if I shutdown/log out etc. However, if you don't have nitrogen installed then this probably isn't your problem but this might help someone.