Same thing happens sometimes with Opera's detached windows or thunderbird's message windows. Sometimes they just seem not to be drawn, but are still there on page switch. When updating the layout then again (e.g. by resizing it or by adding a term), the “missing” windows are drawn again. Maybe it has to do with ReconfigureNotifys sent by Gnome apps? The handling of the WM hints belonging to those seems very weird to me.
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