Set the window compositor to make inactive windows transparent, turn off "New window focus", and spawn a new window. The window will be opaque even though it is unfocused, and will become transparent if focused and unfocused again.
Another way to reproduce this is to set the panel to be transparent, turn on "Make active panel opaque" and log out and in again. The panel will be opaque even though it is inactive, and will become transparent if the mouse cursor is moved over and off it again.
Focus is indded WM related, but the panel manages its opacity by itself, so the second part is a panel bug.
OK, I have made a seperate bug for the panel: http://bugzilla.xfce.org/show_bug.cgi?id=5739