This has been bothering me since the release of 3.0. If using a theme which has a border on the message tray (see image for an example, I used a thick red border to show), the border is still visible when the notification bar hides. While that may sometimes be a desired effect, when watching movies in VLC or playing games or doing any full-screen related activity, the border can become tedious.

Some example css for the above message tray:
#message-tray {
	background-gradient-direction: vertical;
	background-gradient-start: rgba(0,0,0,0.1);
	background-gradient-end: rgba(0,0,0,0.4);
	border: 0px;
	border-top: 2px solid rgba(255,0,0,1);
	color: rgba(255,255,255,1.0); 
	height: 36px;
}



What I think is happening is that Gnome hides the "div" down for the height of it (36px), but it doesn't take into account the border (or the shadow!).

As a quick hack I tried adding the border by using:

#message-tray {
	background-gradient-direction: vertical;
	background-gradient-start: rgba(0,0,0,0.1);
	background-gradient-end: rgba(0,0,0,0.4);
	border: 0px;
	box-shadow: inset 0px 2px rgba(255,0,0,1);
	color: rgba(255,255,255,1.0); 
	height: 36px;
}

This results into the same as above. But finally I was able to cook up a css hack to fix it:

#message-tray {
	background-gradient-direction: vertical;
	background-gradient-start: rgba(0,0,0,0.1);
	background-gradient-end: rgba(0,0,0,0.4);
	border: 0px;
	border-top: 2px solid rgba(255,0,0,0);
	box-shadow: inset 0px 2px rgba(255,0,0,1);
	color: rgba(255,255,255,1.0); 
	height: 36px;
}

The important lines are
border: 0px;
border-top: 1px solid rgba(255,255,255,0);
box-shadow: inset 0px 1px rgba(255,255,255,0.15);

The first one hides the border, the second one makes a 1px invisible border (using a color with the alpha value of 0) on top and the third one uses box-shadow to draw a fake border using shadows. Because we made the 2px invisible border-top Gnome somehow decides to properly hide the box-shadow.

Sadly I could attach just one image, but I will try to illustrate it further and cooperate for this to get resolved.