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The main problem here is that the zoomed_inset_axes returns an axes located at plot time and the twin functions replicate it without copying the locatable properties so it defaults to the normal axes location. The HostAxes in mpl_toolkits is a better choice and will give the expected behavior as it correctly performs twin operations using a parasite axes.
PR #2805 changes zoom_inset_axes to give that axes class as default and you will get the expected behavior
Alternatively, you can get this by calling zoomed_inset_axes using the axes_class argument with
Seen here:
http://stackoverflow.com/questions/13385924/adding-a-second-y-axis-to-an-inset-zoom-axes
On version 1.2.0, this is all fine and dandy:
The unexpected behavior happens here:
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