I agree with you, but I suppose this happens 'cause emerald is not yet fully initialised when Compiz start.
In facts if I set Compiz to use Kwin instead of emerald, I don't need to restart fusion-icon.
Everything works just the way it should from the beginning.
Let me know if it works for you.
Are you also expecting video flickering in avi video?
I use kwin instead of emerald anyway, so still no go for me. Strange.