In FS9, we noticed that, even if you change the wind, the ATC will not udpate the runways in use. You need to reset the AI traffic. It's possible to do that in two ways: either go to the World->Airport menu and select JFK again, or simply put your time acceleration to 8x and then immediately back to 1x. Either action will trigger a whole AI reload, putting the runways in use.
However, it might well be we mis-matched the approach files in the FS9 version...we'll check it as soon as possible. You can verify this by using the default GPS and see if the Canarsie path is displayed for the 13L approach.