The ylabel of the new axes is not vertically centered and sometimes it overlaps yticklabels. This happens in recent development versions but not in 1.2.0.

This script shows the issue:

#!/usr/bin/env pythonimportmatplotlibasmplmpl.use('agg')importmatplotlib.pyplotaspltimportnumpyasnpx=np.arange(100)y1=xy2=1./ (x+1)plt.plot(x,y1)plt.ylabel('Y axis #1')plt.twinx()plt.plot(x,y2)plt.ylabel('Y axis #2')plt.savefig('test.png')plt.close()

This is the ouput with mpl 1.2.0 (correct):

And with 1.3.x (incorrect):