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After realizing this problem is caused by Gazebo and not by robot_localization i found out that the problem is caused by an error in the gazebo tutorials here Gazebo tutorials. In the differential drive plugin section the parameter is written as publishOdom but it needs to be publishOdomTF.

I know that this now transitioned to a gazebo related question and/or answer and should be over at the gazebo forum but still want the information to be somewhere.

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