Please refer to the messages under "Detecting GUI mainloop running in IPython" on http://news.gmane.org/gmane.comp.python.ipython.devel.
At least at the moment, they are not showing up as a single thread; maybe it takes a little time for the thread logic to sort out the messages.
I hope that someone with better understanding than mine of gui mechanics will join the discussion on the ipython-dev list. The IPython people have been making changes, and have more in mind. This involves critical mpl functionality.