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I have actual found the solution to my laser scan shifting problem. The issue was not related to the way that I configured the ekf_localization_node. It actually was related to the odom_alpha parameters of the amcl node that I was launching separately. If your odometry source is not very precise, then modifying the odom_alpha parameters to make them larger in the amcl node can compensate for that in localizing the robot within the map. More details can be found here.