The problem comes from the unnecessary use of computer controls. The Heating, Ventilation, and AC (HVAC) unit is a computer module that "loses its mind" when it or the battery is disconnected. Simply replacing the battery will require this module to be recalibrated.
The following is from memory, so if it doesn't work, check the service manual for the proper procedure. Also, you're lucky the AC works. If it doesn't work, you can't complete all the following steps. Then you just get to look at the flashing lights for the rest of the life of the vehicle.
First, start the engine and bring it up to normal operating temperature. Place the system in the air conditioning mode, but put the temperature control on full HOT.
The engine must be running for these steps. Look at the six push buttons on the control panel. The three in a vertical column on the left side are the first ones to look at. Press the top and bottom buttons at the same time for about five to ten seconds until the two yellow leds start to flash alternately. This will continue for about a minute. During this time, the module is running all the vent and temperature doors through their range and taking voltage readings from the position sensors. These sensor readings will be put in memory so the computer knows exactly how far to move a door when you select partial floor and partial vent. (I do this on my '88 Grand Caravan with a lever, not a computer).
When the lights either stay on or flash together, press one of them to exit the procedure. The easy half is done.
If none of the lights are flashing now, stop! Or, if it was lights on the lower row of buttons that were flashing before, continue. This next step can be frustrating so don't do it just for fun.
If you ignore those two top left buttons, just look at the four in a row along the bottom. Remember, the engine must be up to normal temperature, AC must be operating properly, and the temperature control must be on HOT. Of those four buttons, press the second and fourth one at the same time until the two leds start to flash alternately. As soon as they start to flash like that, move the temperature control to full COLD. If the leds start to flash differently, count your blessings; you're done! Press one of the buttons to exit the procedure. If they don't stop flashing, you'll need to do the same procedure over, ... And over, ... And over, until it passes. Twenty times is my record before it passed.
The module is looking for an 80 degree temperature drop within twenty seconds to calibrate the in-dash temperature sensor. This is usually pretty easily accomplished as long as the AC is working. Typical duct temperature under full heat is over 140 degrees, and ideal temperature under full AC / cold should be around 40 degrees. If multiple attempts to pass this procedure fail, try repeating it immediately after a ten minute drive at highway speeds. These radiators are so efficient that they may reduce engine coolant temperature too low even without the electric radiator fan turning on. Driving on the highway will bring the engine temperature up for a higher starting point.
Tuesday, March 24th, 2009 AT 2:14 PM