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I solved! I moved the skeleton tracker initializer:

niteRc_ = userTracker_.create();
if (niteRc_ != nite::STATUS_OK)
{
  ROS_FATAL("Couldn't create user tracker");
  ros::shutdown();
  return;
}

after setting the RGB and the DEPTH modes. If you are interested, the code is available here. The node is an extension for the openni2_tracker. The node tracks the skeleton and publishes rgb stream, depth stream and point cloud. Furthermore the node publishes a topic with the IDs of the tracked users.