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0e1f616
(Get the code!)
I can confirm that this happens when the launcher thinks you're dragging something. I could reproduce it with QtDesigner
Click to drag a widget from the widget box, at that moment the launcher becomes visible. Then let the widget fall back into the widget box. The launcher stays on top, still responsive. Then click another windows, for example firefox and you'll be clicking through it.
Go to nautilus, drag an icon, let it drag immediately back where it came from and the launcher disappears again.
So Mark: "I think we need to drop the "non-autohide" mode entirely, and that will
make it easier to ensure the launcher can't think it should be
always-visible, ever."
I don't think this would make any sense in this case as it is not thinking it should not stay on, it is just waiting for a drag-drop. Apart from that we should not lose any more options to personalize unity.