If there is a new API that fedex has rolled out for different rates then there is a good chance we aren't using it. Alternatively, these fedex APIs sometimes need additional information in the API requests that aren't being included which may be why the rates aren't being calculated the way they are on their site.
Looking through the codebase we aren't doing anything special when sending requests, and then there must be an issue with the way active_shipping is submitting rate requests.