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Ah, you've stumbled upon the ol' "in what frame is IMU data reported" issue. See these:

http://answers.ros.org/question/50870/what-frame-is-sensor_msgsimuorientation-relative-to/
http://answers.ros.org/question/200480/imu-message-definition/
https://github.com/ros-infrastructure/rep/pull/95

In ekf_localization_node, I assume the frame_id in the message is the frame in which the sensor is mounted, so you should produce a base_link->imu transform (try using static_transform_publisher).

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