I noticed an issue related to PolyCollections and all Agg backends. If the linewidth keyword is set to 0, then the entire Polygon patch is not shown, rather than removing only the border line. This happened with MPL release 1.4.1, because 1.4.0 works as expected. I see the same behavior on Python 2.7 and 3.4 from Gentoo Linux and in an Anaconda 3.4 environment. I ran a number of tests and posted them to Matplotlib-users. However, as a simple expample::

import numpy as np
import matplotlib.pyplot as plt

x = np.linspace(0, np.pi*2, 1000)
y = np.sin(x)

# Change the lw != 0 and this works fine
plt.fill_between(x, y-0.1, y+0.1, lw=0)
plt.show()