I noticed this same problem on my Droid Incredible after it got its Gingerbread update. Now I see it on the Galaxy Nexus. Randomly (as far as I can tell) when I am using an application and hit the Home button, I get a blank home screen with only the App Tray button showing. Then about 1-3 seconds later, all my icons appear.
I looked around on the web, but couldn't find much about this. Does anyone know what causes this? Anyway to fix is or make it better?