E.g. JDownloader and some other apps produce a black square on the upper left desktop. This can be removed by deactivating the composer or exiting the panel. For further information: http://forum.manjaro.org/index.php?topic=8638.0
Btw. it's relavitely small, the square
That "square" (its more a rectangle on my system) also appears when using java programs in xubuntu 12.04 and 14.04b1. And it's not a black box in my case - it depends on the theme. I for example use the acid theme (http://sixsixfive.deviantart.com/art/ACID-280889262) and therefore the box is gray because it's just the upper left few pixels of the window title-bar.
This bug is caused by any java application which creates a notification icon (aka old-style gnome system tray). As a workaround you can simply disable the tray icons in each program. eg JDownloader allows this.
This bug seems to have stopped happening for me. We haven't fixed anything in Xfwm afaik. Maybe it was a java bug all along?
Disregard previous comment, it still happens.
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