Yes, you found a small bug. We haven't uploaded the updated AFCAD with removed jetways for JFK2. However, you can quickly fix this by letting the GSX Control Panel create an Exclude file for you.
- Open the parking customization page at JFK.
- Click the Exclude radius checkmark on any parking with a jetway. It's likely already clicked so, you must click it and click it again, to trigger the creation of an exclude file.
- Quit the simulator and open the GSX Control Panel, you should see an exclude XML for JFK ready to be compiled.
- Compile it and restart the sim, the orginal jetways should disappear.
Of course, I'll upload the fixed AFCAD right now.