A couple more things to look at is sometimes you don't get the probe plugged all the way into the controller, and it gives a bad connection and a bad temperature reading. Also if you put the probe too close to the food, it can make the probe read lower. Lastly, if it is the standard dome thermometer, I wouldn't trust it, they can go bad at any time, if it ever worked in the beginning you should feel lucky. But you did say your cooks are taking longer.
XL Big Green Egg, Weber kettles, WSM 22.5" and Pellet Pro adapter