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From here :
robot_pose_ekf publishes transforms from odom_combined to base_footprint.
Sometimes an urdf will have base_link as the root of the tf tree, with base_footprint as a child. Since robot_pose_ekf has a hard-coded output transform (odom -> base_footprint), then this combination will break the tf tree (base footprint will have two parents) and it could explain your issues.
Even if you don't have an urdf, you cannot use robot_pose_ekf in its current state, and have any other tf publication with base_footprint as the child.