Originally Posted by gmanjeep
Is the Actuator controlled by Vacuum or Electronically? It just seems weird that this all started after the battery went dead.
Its electronically controlled.
When the battery is disconnected sometimes the gear in the air mix actuator meshes incorrectly with the other gear and brakes when you reconnect the battery. It cycles back and forth in normal operation upon start up of the car. When the gear brakes the A/C controller reads a fault and puts out a visual on the display making the display blink every time you start the car.
on avoiding this in the future would be to turn off the A/C system before disconnecting the battery. This way when you reconnect the battery the air mix actuator will already be in the correct position.