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 python
import matplotlib as mpl
mpl.use('agg')
import matplotlib.pyplot as plt
import numpy as np
x = np.arange(100)
y1 = x
y2 = 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):

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:
This is the ouput with mpl 1.2.0 (correct):

And with 1.3.x (incorrect):
