I think there are a number of factors here.
1) You're always going to get better braking with the revs up, as it will create a stronger longer lasting vacuum.
2) when you are braking with your left foot it is used to using the clutch and therefore is not as sensitive as your right foot. As such, trying to compare the two is quite difficult.
If you're brake pedal is stiffening up when the engine is off then I don't think you have a problem, you are just realising how good left foot braking is

Just my tuppence worth

Paul