The summary lines are wrong, aren't they, the weight gain and calorie difference don't equate?
They are not, but I can see why you might think so.
Digesting food requires energy, the Thermal Effect of Food and in this simulation this is taken from the Glycogen stores.
So when looking at Protein and Fat eaten the Difference column and the Total body weight column (which is the change in the summary lines) should always come out as the number of calories in a pound of body fat. If no exercise is being performed.
When looking at carbs the energy derived and the cost both affect into the glycogen column, so the energy derived and the cost of the digestion partially cancel out the changes to the total glycogen level.
The calculator also has different digestion costs for converting carb to glycogen and fat, with the conversion to fat being significantly more expensive. This means that once the body's maximum glycogen level is hit some carbs go to glycogen and some to fat with varying costs.