title: plant.SetPositions does not update visualization
body: <p>My code (using Russ Tedrake's <a href="https://github.com/RussTedrake/manipulation/blob/bead198553d328bb2faeba5c22b493104dbf7657/manipulation/scenarios.py#L138" rel="nofollow noreferrer">manipulation module</a> to make shapes): <a href="https://gist.github.com/richardrl/b71a1b6ed9e30dfc9ac252cc99193634" rel="nofollow noreferrer">https://gist.github.com/richardrl/b71a1b6ed9e30dfc9ac252cc99193634</a></p>
  <p>The logic is in line 147 is completely ignored with respect to the visualizer. No matter what positions I set it, the visualization is the same.</p>
  <p>Video here: <a href="https://www.dropbox.com/s/86werg0fxmbqebs/ball_horizontal_line.mp4?dl=0" rel="nofollow noreferrer">https://www.dropbox.com/s/86werg0fxmbqebs/ball_horizontal_line.mp4?dl=0</a></p>
  <p>The spheres pop out of the origin position (which they start off in from AddShape) and move outwards in a horizontal line, regardless of what configuration I set in line 147.</p>
  <p>I am not positive whether this is a problem of, the visualization is disconnected from my plant, or something else. But what I do know is my code is setting the plant positions properly (console outputs):</p>
  <pre><code>ln145 before setting positions
  [ 1.  0.  0.  0.  0.  0.  0.  1.  0.  0.  0.  0.  0.  0.  1.  0.  0.  0.
    0.  0.  0.]
  ln156 after setting positions
  [ 0.          0.          0.3         0.          0.          0.          0.
    0.6         0.          0.3         0.          0.          0.          0.
    0.3         0.          0.81961524  0.          0.          0.          0.        ]
  ln163 after simulation
  [ -2.48258262e-04   0.00000000e+00   2.99999898e-01   0.00000000e+00
     9.32950273e-04   0.00000000e+00   2.98500000e-01  -2.25902431e-01
     0.00000000e+00  -6.31659664e-01   0.00000000e+00  -1.30262016e+00
     0.00000000e+00   2.98500000e-01  -7.89982679e-01   0.00000000e+00
    -3.71132816e-01   0.00000000e+00   1.28836582e+00   0.00000000e+00
     2.98500000e-01]
  </code></pre>
  <p>EDIT: Here is a self-contained file that reproduces the error: <a href="https://gist.github.com/richardrl/6013299b63100c585851ed1803406cfa" rel="nofollow noreferrer">https://gist.github.com/richardrl/6013299b63100c585851ed1803406cfa</a></p>