The following script demonstrates the issue with Matplotlib 1.3.1:

import pylab as plt

X = 5  # set X = 0 and matplotlib drops all later points

data1 = [1,2,3,4,5,6,7,8]
data2 = [1,2,3,4,X,6,7,8]

f = plt.figure(0)
plt.scatter(data1, data2)
plt.xscale('log')
plt.yscale('log')
plt.show()

The problem occurs when using a scatter plot with logscaled axes; if zeros are present in the data, a substantial fraction of the points are discarded. Obviously zeros can't be displayed on a log plot, but I would have expected those points (and only those points) to be silently dropped, or at worst an exception be raised.