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The heater boxes are mis-adjusted. My 3.2 with SSIs work exactly as required. With the heat levers full down, there is 0 heat coming out of the vent system. With a single heat lever, logic would dictate if there are 2 heaterboxes, the cable has to somehow split to activate both heat boxes. My thoughts are either one segment of the heater cable is either broken, leaving one heater box on and one shutting off. The reason you might be noticing the heat now, is the SSIs are incredibly effective and when you put them on, the broken heater box control became evident.
You don't need a mechanic to check your heater boxes, jack the car up, jack stands and look at the end of the heaterhoses for a star looking opening in a box. Verify both boxes are in the same position.