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I have also had this occur a couple of times since the 2.0 upgrade on my windows 8 (64-bit) system. I am running the 32-bit Portable version of Calibre.
If I move the Window aside then I can continue using calibre. The orphan Window(s) will not disappear until I exit Calibre. Unfortunately I cannot seem to reproduce it at will which makes gathering diagnostics a little harder.
I remember it used to happen in much earlier versions (0.x series) of Calibre with some frequency. However at some point changes meant that it stopped happening. I have not seen it for some time now until this 2.0 release.
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