I have created a runnable sample app that demonstrates the problem

Here is a much simpler 10 line sample that doesn't require wxPython and demonstrates the problem:  you can't pick the red line.  This seems like a bug in mpl 1.0.

import matplotlib.pyplot as plt

fig = plt.figure()
ax = fig.add_subplot(111)
ax2 = ax.twinx()

line, = ax.plot([1,2,3], 'r-o', markersize=15, picker=5) 
line2, = ax2.plot([4,2,12], 'b-o', markersize=15, picker=5) 

def onpick(event):
    print 'picked line: ', event.artist

fig.canvas.mpl_connect('pick_event', onpick)

plt.show()