I have very similar problem as here. However, my default backend environment is correct for both python 2.7 as well as 3.6.
import matplotlib
matplotlib.get_backend()
...gives me TkAgg and GTK3Agg respectively.
I haven't used python on this machine for months so I do not know exactly when this behaviour changed. I have used matplotlib before on this machine and it worked just fine.
Any suggestions to solve this?