It seems that once a .3dm is loaded which contains an open Notes window, or more importantly, when Rhino is closed from a document with an open Notes window, the next time Rhino is opened, even before a file is selected, the Notes window is already open. Perhaps this is by design, but it seems to me that Notes are document things and should only appear when a document containing them is opened. Perhaps there are other windows that display this characteristic - windows that show document related things, but stick around as Rhino instance things.
Maybe the idea is to store their location between Rhino invocations. I think this should be part of the document.
Or maybe it’s just a bug. 09/22/2015 WIP and earlier.