I'm using matplotlib 1.3.1 with GTKagg backend. I found that if I call ax.set_xscale before calling ax.scatter everything works fine. However if I change the order of the commands, most points are not displayed. Here is some sample code:

fig, ax = plt.subplots(1, 2)
n = 1000
x = np.abs(np.random.laplace(size=n))
y = np.arange(n)
ax[0].scatter(x, y)
ax[0].set_xscale('log')
ax[1].set_xscale('log')
ax[1].scatter(x, y)

This leads to the following output: http://imgur.com/xqsR9fr

I'm not sure if this is the same as #2872 or not, maybe someone who has the current master installed can test that.