Comment 1 for bug 1081674

This is a consequence of how unity-2d draws itself on screen. Effectively it creates a window that covers your entire desktop & all open applications windows on your screen, then specifies to X the bits it wants to be transparent (using XShaping). The compositor (metacity in this case) then takes this info to draw your desktop.

The tool you're using to grab screenshots unfortunately is not aware of XShaping. I would encourage is the use of another screenshotting tool. gnome-screenshot is capable, and should be scriptable in a similar way to xwd.

Alternatively you could try turning off metacity's compositor, logging out & in again. Unity-2d will fall back to a different XShaping routine that may work better with xwd. Try this with:
gconftool --set --type bool /apps/metacity/general/compositing_manager false