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Started out as a comment, but will add a few things:

1. Can you please post (a) your launch files and (b) some sample input messages (as text)?
2. You said your coordinate frame has forward and right as positive, which is incorrect. REP-103 specifies +X as forward and +Y as left.
3. Instantaneous velocity, if driving forward, will always be positive, no matter which way your robot is facing. This is correct. The filter converts velocities from the robot's body frame to the world frame internally. As far as the EKF output goes, the ROS nav_msgs/Odometry message specifies that the output pose data is in the world frame (header.frame_id in the message) and the velocities are in the body frame (child_frame_id in the message).
4. Looking at your configuration image, you are fusing both your calculated pose and velocity from your wheel encoders, but those both come from the same source. You're effectively feeding the filter the same information twice. It doesn't hurt it necessarily, but I'd give it one or the other.
5. You are fusing yaw from both your IMU and odometry. Those are going to diverge, so you'll have to turn one of them off.