First I would start by feeling the heater hoses/pipes going to the heater core (engine warm). Feel if they're both hot to make sure it's not a faulty engine thermostat. Make sure the coolant is up to full. Could be a faulty heater vent door too. Sure it might be a hvac controller, but usually problems are small things ...or at least look at the small things first. Dealer might have 'thought' it was the controller last time, but then after installing it, turned out to be something else. How often does that happen?! Well guess, what they're probably not inclined to remove it, esp if they replaced multiple things and they weren't sure if it was a controller or not (sometimes controllers can be intermittent). They're just going to say it was the controller when it 'may' have been a $20 vent motor that was also replaced. Or maybe in your case it WAS the controller.
You could probably use AlfaOBD software (see 4th Gen DIY Forum) to scan yer truck and HVAC to get the codes and run it through it's paces (articulate vent doors, etc). Or another scan tool with good capabilities. As far as I know they don't need to be 'paired' with the main computer ...but I guess I'm not 100% sure. With a good scan tool there should be a 'cycle' mode where it'll run the motors through their range. If something doesn't move, then you'll know it's faulty.
Is the system acting (now) the exact same way it was acting before you installed the controller?