Not sure what the problem could be. I would take the controller off carefully and check for a loose connection and correct. Also make sure the jack for the probe is tight. Turning the smoker off and unplugging then plugging it back in and turning it on may reset it. If none of that works, contact Steve. Good luck.
EDIT: There is another possibility, although rare. Make sure that your food does not touch the box probe. There have been a couple of instances where someone managed to skewer the meat on the box probe. Rare but it has happened. Also, when using the meat probe, beside to program in the finished temp that you want the meat at. Say you set the smoker temp for 225 and the meat temp for 195. All the other steps should be 0.