Close a tkinter progressbar window while matplotlib window is open
You are getting conflicting gui-main loops between the TK you are starting and the TK that plt is start. If you want to use matplotlib with your own gui, you must embed it your self and you can not import pyplot. All the behind the scenes magic that makes the pyplot interface wonderful is what is messing you up here.
For a tutorial see here, for how mpl does the embedding see here.
Also see: