2006 Mercury Marquis Vent control

The mode selection is done through a series of air doors that are operated by vacuum. When there is either a partial or total loss of vacuum, the system will default to either defrost or on some vehicles, heat. Acceleration can also have an effect on the doors for the same reason.

Look under the hood for a small black plastic hose coming through the firewall. Follow it to the vacuum source looking for any breaks, cracks or leaks. Also follow any other lines that branch off because they may go to a vacuum reservoir (storage tank) and a leak there will cause the same problem. Using a vacuum gauge to determine if you have full vacuum at any given point is the best way to find it. You can cut into the line anywhere and splice it back together with a piece of vacuum hose. Find the broken line, you found your problem.

This model does have a lot of problems with the controller also but check the vacuum first

I agree with Wrenchtech, welcome aboard wrenchtech, I have one thing that can alay your fear of replacing a good controller, try this test and reset procedure, let us know what codes display on the controller face.
Electronic Automatic Temperature Control Module Self-Test à   The EATC module self-test will not detect concerns associated with data link messages like engine coolant temperature or vehicle speed signals. A scan tool must be used to retrieve these concerns. à   The EATC module self-test will detect concerns in the system control functions and will display hard DTCs in addition to intermittent diagnostic trouble codes for concerns that occur during system operation. The vehicle interior temperature should be between 4 °-32 °C (40-90 ° F) when carrying out the self-test. If the temperatures are not within the specified ranges, false in-vehicle temperature sensor DTCs will be displayed. à   The self-test can be initiated at any time. Normal operation of the system stops when the self- test is activated. à   To enter the self-test, press the OFF and FLOOR buttons simultaneously and then press the AUTOMATIC button within 2 seconds. The display will show a pulse tracer going around the center of the display window. The test may run as long as 30 seconds. Record all DTCs displayed. à   If any DTCs appear during the self-test, follow the diagnostics procedure given under ACTION for each DTC given. à   If a condition exists but no DTCs appear during the self-test, GO to SYMPTOM CHART Condition: The EATC System Is Inoperative, Intermittent or Improper Operation. à   To exit self-test and retain all intermittent DTCs, push the blue (cooler) button. The control will exit self-test, retain all intermittent diagnostic trouble codes and then turn OFF (display blank). à   To exit the self-test and clear all DTCs, press the DEFROST button. The vacuum fluorescent display window will show 888 and all function symbols for one second. Then, the EATC control assembly will turn OFF (display blank) and all DTCs will be cleared. à   Always exit the self-test before powering the system down (system turned OFF). à   Intermittent DTCs will be deleted after 80 ignition switch ON cycles after the intermittent condition occurs. Electronic Automatic Temperature Control (EATC) Module Cold Boot Process The purpose of the cold boot process is to allow the EATC module to reinitialize and calibrate the actuators. To carry out the cold boot process, follow the steps below. 1. Turn the ignition switch to the OFF position. 2. Disconnect the EATC module electrical connectors. 3. Wait one minute. 4. Connect the EATC module electrical connectors. 5. Turn the ignition switch to the ON position. 6. Select any position except OFF on the EATC module. The EATC module will now initialize and calibrate the actuators. Calibration of the actuators will take approximately 30 minutes.