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Lets start at the beginning, it looks to me that both python and c++ use the same underlying subscription.cpp/hpp code in rclcpp and for python its just wrapped. If i'm wrong thats the issue.

That's the issue. rclcpp and rclpy are both wrapping a C library called rcl. A change in rclcpp won't affect rclpy.

There's a helpful diagram on this page: http://docs.ros2.org/eloquent/developer_overview.html#internal-api-architecture-overview