The problems are in HVAC-Calc, but I imagine they may exist if Wrightsoft or Elite was used.
Problem 1: Fireplaces
The software offers three options which in one room come out to 3500btu/hr, 7000btu/hr, and 20,000btu/hr. Without the fireplace the room in around 11,000btu/hr; the fireplace is a large percent of the total. The house has two fireplaces and the total could range from 5% to nearly 30% of the total heat lost.
Problem 2: Floors over unconditioned basement
The loss if the basement is unconditioned is huge. However, the basement is usually temperate, probably the result of duct leakage. In the future new basement ducts may change that. In either case, the basement won't be heated to the same setpoint as the other conditioned spaces.
Problem 3: Duct leakage
Again, HVAC-Calc is only providing a few options. They would always be running through areas with lower setpoints or areas that are unconditioned. To some extent it is intertwined with the floors over the unconditioned basement.
The basement could be turned into conditioned space. However, that would inaccurately model the individual rooms above it.
What is best way to handle it? Do the two MJ8 packages handle it much better?