I'm not exactly sure when I first noticed this (I had put it down to the early nature of the 64 bit version), but in both the 64 and 32 bit OS X versions, when you first open PixInsight, open an image, and then Duplicate it - the active window is behind the now inactive original image. This occurs for every subsequent Duplicate. Sometimes opening another image into PixInsight solves this, sometimes not (the image opened will fall in behind of the inactive windows). When it does solve it, Duplicating images behaves normally for the remainder of the time that PixInsight is running.
John