How big is the "mystery" window? If its a relatively small square, then it might be the streaming dragon window (the one that shows how much data is queued up to be streamed). I've had it in the past where even the non-streaming client can still have that window present but invisible and it could in theory be blocking things.
Can you right click the invisible window and get its options at all? IIRC the streaming window doesn't act like a normal window with the usual complement of options too, it just kind of sits there in the way.
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