To reproduce, you need a dual-monitor setup. I'll refer henceforth to "left" and "right" monitors.
Select an empty desktop. On the left monitor, launch a Thunar window, and then a Terminal window. Set the Terminal window to Fullscreen mode. As it has focus, it should now hide the non-full-screen Thunar window.
Now move your mouse cursor to the right monitor, and click anywhere (easiest is to click the wallpaper). Notice Terminal on the left monitor losing focus. Keeping your mouse cursor in the right monitor, Alt-Tab to Thunar. Despite gaining focus, Thunar will remain hidden behind the full-screen Terminal.
This misbehavior appears consistently across all desktops, and also occurs if we switch the left and right monitors in the example above. Tested on a fully patched Fedora 17 XFCE spin.
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