Comment 14 for bug 147426

There is a setting somewhere in xine, something about keeping it in the foreground (always_layer_above in the gui section). Unchecking that works around the issue but obviously stops stupid popups from being hidden.
In a somewhat related matter, having always_layer_above enabled will keep xine above the popups but still give them keyboard focus, resulting in *really* akward behaviour. I personally consider the always_layer_above option too buggy to use because of this.