Shoutbox

The windows are actually in the same position, as the steath skin hides the windows border at the top so that's why it won't hug the top or edge of the screen (this is easily visible if you flick quickly between your two screenshots)

I suspect that the skin may automatically set the width of messenger, in which case there's nothing you can do about it, but you may be able to re-size it vertically so that it doesn't overlap with your steam window