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The calculation sequence looks like this:

Simulate tower at full speed
IF (Setpoint exceeded) THEN
  Simulate tower in free convection mode
  IF (Setpoint not met) THEN
    Simulate tower at min fan speed
    IF (Setpoint exceeded) THEN
      Simulate tower cycling between min speed and free convection
    ELSE
      Find airflow ratio between min and max that meets setpoint
    ENDIF
  ENDIF
ENDIF

To simulate the tower in free convection mode, the program takes the results from the full speed simulation and multiplies the operating range by the Fraction of Tower Capacity in Free Convection Regime input field. Note that it does not run the tower curves at a "free convection airflow ratio" to do this. So the airflow ratio in the free convection mode is irrelevant. Also, if you are not careful, you could specify a free convection capacity that is higher than the capacity at min fan speed, which would give you some funny numbers.

The negative curve outputs probably has to do with the creators expecting that the curves wouldn't be used at such a low ratio. If your min fan speed is above 0.15, then you'll not get negative numbers. You're right in that it has nothing to do with free convection.