When a windows is using OpenGL, like xmms visuals, or a movie, like mplayer, the
window will always be on top. The window can lose focus, but it will continue
to be on top of all other windows. This happens with beta1, but I think it also
happened in 4.0. My XFWM4 is build with the composite extenstion.
That's a probmem with the composite extensions and your libGL, it's not a
problem with Xfce.
Either disable the composite extension or run xfwm4 w/out the compositing manager.