On relatively flat terrain, the cruise control maintains the car's speed pretty constant, without overshooting or undershooting the set speed. Under these circumstances, you are probably achieving optimal FE. Under manual accelerator control, the car's speed tends to drift up and down. Each time the car's speed changes [either up (accelerating) or down (decelerating)] there's energy flow taking place [either from the ICE/battery or to the battery] because the car's kinetic energy is being increased or decreased (but its potential energy is not changing since its altitude stays approximately constant). Since the ICE's FE drops when the car is accelerating, and since regenerative energy recovery is not 100% efficient, the best general strategy for maximizing FE is to keep the car's speed constant. I think that this may be why you're finding better FE when you use the cruise control.

Stan