I did not order my jeep with automatic air control, however I do have it on my wife's 08 Highlander and the way it works is that it keeps the temperature in the vehicle to the temperature you set it to. It will automatically pick whatever vents it thinks it needs to get to the desired temperature as quick as possible. I find it annoying because of what you say. It'll pick different vents and different fan speeds. The only time it works good is if you are in the car for a long trip and you want to keep the temp in the car a certain temperature.
Other than that I found myself fighting the auto temperature because air would blow through a vent I didn't want or fan speed is not what I desired (too high or too low) we don't use the automatic feature.