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Looking at pr2-empty-amcl.launch:

<launch>

  <!-- start up empty world -->
  <include file="$(find gazebo_worlds)/launch/empty_world.launch"/>

  <!-- start up robot -->
  <include file="$(find pr2_gazebo)/pr2.launch"/>

  <!-- Tug Arms For Navigation -->
  <node name="tuckarms" pkg="pr2_tuckarm" type="tuckarm.py" args="b" output="screen" />

  <!-- load map -->
  <node name="map_server" pkg="map_server" type="map_server" args="$(find gazebo_worlds)/Media/materials/textures/map_blank.png 0.1" respawn="true" />

  <!-- nav-stack -->
  <include file="$(find pr2_2dnav_gazebo)/2dnav-stack-amcl.launch"/>

  <!-- for visualization -->
  <include file="$(find pr2_navigation_global)/rviz/rviz_move_base.launch"/>

</launch>

Is it possible that you didn't launch one of the nodes?

Looking at pr2-empty-amcl.launch:

<launch>

  <!-- start up empty world -->
  <include file="$(find gazebo_worlds)/launch/empty_world.launch"/>

  <!-- start up robot -->
  <include file="$(find pr2_gazebo)/pr2.launch"/>

  <!-- Tug Arms For Navigation -->
  <node name="tuckarms" pkg="pr2_tuckarm" type="tuckarm.py" args="b" output="screen" />

  <!-- load map -->
  <node name="map_server" pkg="map_server" type="map_server" args="$(find gazebo_worlds)/Media/materials/textures/map_blank.png 0.1" respawn="true" />

  <!-- nav-stack -->
  <include file="$(find pr2_2dnav_gazebo)/2dnav-stack-amcl.launch"/>

  <!-- for visualization -->
  <include file="$(find pr2_navigation_global)/rviz/rviz_move_base.launch"/>

</launch>

Is it possible that you didn't launch one of the nodes?nodes? If you launch each of these nodes by hand, does the navigation stack work for you?