Huh, that is a weird problem.
I would remove the radio console and check that the damper control knob is working properly. With the radio and front trim out, you'll get a good view of the gears and pull cable that the knob actuates. Maybe the cable is opening the wrong vents?
I guess the other thing to check is that the ductwork past the heat exhanger is connected properly. If it was disconnected somehow, that might explain how the bottom is warm (since all the ductwork is located around there, but the top is cold. I have never heard of that happening, but anything is possible, I suppose.
I guess just check out as much of the HVAC system as you can behind the dash. Do you have a cabin filter? You can remove the glovebox assy and check that out as well, along with the blower.