see the screen shot below
More than a year and this is not fixed? Come on! :(
This is because kwin draws a shadow under it! if you disable the shadow effect, this will stop happening! but of course, who wants to disable shadows?
A work around is to create a window rule and force gnome-do to be treated as a dock/panel
Bug watches keep track of this bug in other bug trackers.
More than a year and this is not fixed? Come on! :(