Why do the air changes per hour reported not match exactly with the values entered in model data?

The difference in air changes per hour (ac/h) between the sum of mechanical and natural ventilation and infiltration values you entered on in model data and the values reported in simulation results is caused by the method used to calculate and report ac/h in EnergyPlus v4 and later. The new way of reporting ac/h includes consideration of the air density and the exact air change rates reported will depend on the density (temperature) of the outside air being introduced into the building relative to the density of the zone air.

More specifically, the design volume flow rate entered in ac/h is converted to mass flow during the simulation using the current outdoor air density.  The simulated mass flow rate is then reported back out in indoor air density (for infiltration and natural ventilation) or EnergyPlus standard air density for HVAC system outside air, neither of which will ever (or extremely rarely) match the outdoor air density.  So, the ac/h outputs will never exactly match the inputs.