By default, ESHA does not calculate Calories based on 4-4-9. The Food Processor determines Calorie totals by adding up the Calories of the individual foods in a Recipe (or Person).
Per the FDA regulations for U.S. foods, the sources of the individual ingredients can use one of six different methods for determining Calories. The various ingredients in your Recipes may have used more than one of the acceptable Calorie calculation methods. The ESHA Calorie totals reflect this.
The six methods for calculating Calories for Nutrition Facts panels as described in The Code of Federal Regulations (CFR) are: 4-4-9, Atwater factors, 4-4-9 minus insoluble fiber, specific food factors approved by the FDA, bomb calorimetry and using general factors for caloric value of sugar alcohols. These are explained in the CFR, section 101.9(c)(1)(i).