I am having exactly the same problem after the upgrade. It sets the inbound final approach course incorrectly with the turn inbound. (My correct inbound course was 249 while the I set the correct course then it periodically (every few minutes) resets to the wrong final approach course (keeps using the same incorrect course) it then sounds a loud tone alarm every 3 seconds and indicates a warning box ("set correct ILS inbound course".) It flies the initial phases of the approach fine (correct courses indicated), just the final approach course. When vectors to final are activated it starts immediately. I have my 5600 linked to a GTN 650. The Garmin indicates the correct course the entire time. The AP will follow the incorrect indication and it makes hand flying the approach difficult.