Notice that the cylinder is OK, but the second shape (a .6x.2x.1 box) is rotated and also white. The URDF file I used is unmodified from urdf_tutorial, and its text is exactly as posted in the wiki.

The first thing I noticed was that the coordinate assignment looks off causing the box to be higher than wide instead of vice versa. So I tried to just put a couple of colored boxes in the x, y, and z directions to see what the proper assignment was. I got as far as one box, the URDF file is this:

<?xml version="1.0"?>
<robot name="R2-D2">
  <link name="base_link">
    <visual>
      <geometry>
	<cylinder length="0.6" radius="0.2"/>
      </geometry>
      <material name="white"><color rgba="1 1 1 1"/></material>
    </visual>
  </link>

  <link name="redbox">
    <visual>
      <geometry>
	<box size=".1 .1 .1"/>
      </geometry>
      <origin xyz="1 0 0"/>
      <material name="red">
	<color rgba="255 0 0 0.5"/>
      </material>
    </visual>
  </link>

  <joint name="base_to_redbox" type="fixed">
    <parent link="base_link"/>
    <child link="redbox"/>
  </joint>
</robot>

...so it's a red box at xyz="1 0 0". This is how it looks like: