UPDATE: Bug is described HERE.
The "problem" still allows functionality. I have 12.04 on a T61 Thinkpad. The indicator/menu bar is rendered correctly on both screens and everything with unity/dash is fine.
The main "problem" is that the icons on my desktop don't show up (normally they are top left) and now they are off the screen. I can see them by going to the Desktop folder (aka /home/$USER/Desktop). If there are more than a couple icons, the later ones start to show up.
Not sure if it matters, but the same thing happens with VGA connection between the external monitor and the laptop, as well as with the docking station and with both VGA and DVI.