Starting with Snow Leopard, Dictionary can have multiple windows open. Also, it now remembers the last window you had open. So when you tell it to look up a word from somewhere else, it launches the app (which reopens all the windows you had open last time you quit) and opens a new one for your definition. I dont know how you missed this solution, but just close the windows and youll be fine. If you quit with them all still open, theyll all still be open next time you launch Dictionary.