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I believe this happens because the changes within the urdfdom package. The parser does not know of the PR2 specific transmission elements. Try running the ROS-I Hydro urdf parser to see this error for yourself:

rosrun check_urdf pr2.urdf

Make sure that it is run in a Hydro environment. If you would like, try parsing it using this file https://github.com/PR2/pr2_calibration/tree/hydro-devel/pr2_calibration_launch/pr2_urdf_parser_py/urdf_parser_py. You may have to hack MoveIt to point towards this parser.

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