Chris, this is what i noticed on your model as well. Haven't had a chance to dig in to better understand why.
My first thought is that it might be the way your lids are defined. You might want to build a simpler model to see if the problem still exists there. IE, a single body model.
I deleted the cold boundary conditions and resolved the problem for just the hot side. The mass flow rate came out right.
I then added on new boundary conditions. I changed my outlet conditions to environmental pressures, temps.
I made my inlet conditions the same.
This time, everything came out reasonable. Im not sure how changing the oulet conditions the way I did resulted in a different mass flow rate which makes me question it.
impossible to determine without knowing what the steps were to create the first one and what changed between it and the second one.
one of the standard "smoke tests" is to do a mass in equals mass out test same with enthalpy. if that is working, i'd go with those. the only way to confirm the results are right is to compare with physical or hand calcs.