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Your frame_ids need some attention.

First, I'd read REP-105. ROS navigation generally assumes that you have three frames:

• map - Your robot's pose in the map frame is meant to be referenced from the map itself, i.e., it should either come from something that's, e.g., matching laser scans to a map, or it could come from an r_l EKF instance that is fusing the output of a scan-to-map matching node. The robot's pose in the map frame should be very accurate, but may be subject to discrete discontinuities ("jumps"). move_base generates its plans in this frame.
• odom - Your robot's pose in the odom frame is usually not referenced to the map, and will drift over time. Your pose estimate in this frame will come from things like wheel encoders, or an EKF instance that is fusing wheel odometry data. This is the frame in which control/local planning happens in move_base.
• base_link (or base_footprint) - The coordinate frame whose origin is (usually) at your robot's centroid, or center of mass, projected into the ground plane.

Your robot's pose in the map frame is given by the map->base_link transform. Your robot's pose in the odom frame is given by the odom->base_link transform. But tf doesn't let you have two parents to the same frame, so we apply some simple transformation math and end up with a transform chain that goes map->odom->base_link.

It seems to me that you are trying to operate just in the odom frame for everything. That's fine to start, and will work well for simulation. However, tf will also be very unhappy if you let two different nodes publish the same transform. In this case, your EKF instance is generating odom->base_footprint. I'm thinking that whatever is generating your wheel encoder odometry is also publishing that transform, so you need to see if the node in question has a parameter to stop it from publishing that transform (most do).

Also, your move_base config is not going to work well, I think. I'd change it to this:

local_costmap:
  global_frame: odom
  robot_base_frame: base_footprint

  update_frequency: 10.0
  publish_frequency: 10.0
  transform_tolerance: 0.5  

  static_map: true  
  rolling_window: true
  width: 3
  height: 3
  resolution: 0.05

global_costmap:
  global_frame: odom
  robot_base_frame: base_footprint

  update_frequency: 10.0
  publish_frequency: 10.0
  transform_tolerance: 0.5

  static_map: true