(1) file heatTransfer.wbpz
In first case, the heat generation input value for last 20 sec (80 to 100 sec) is constant and has a value of 0W, whereas in the other case, it is linearly dropping from 35000W to 0. This clearly explains the reason behind heat flow value being higher on the second case as compared to the first case. If you check out the heat flow chart, you can understand how the values are dropping down.
(2) file EVAL_THERM1.wbpz
I am not able to understand the values 0.434 and 0.604 that you have used in calculating Q. What do they represent and how did you get them? I understood the last term in the equation which is deltaT (800-22=778C).