When you say different positions, I expect you mean different velocities or position changes as if you set the velocity constant, the position will never be constant...

So how different are your velocities? If they are slightly different I wouldn't be worried. If you're running hector_quadrotor with all it's plugins there is a lot (!) going on. For one there are aerodynamics and propulsion plugins that could cause the results to be different every time. The drag and propeller forces are calculated each step and these could vary considerably each simulation. Also are you using ground_truth for pose estimation or the imu? Here again the imu is of course more realistic but less accurate and can cause differences. You can even add wind to the simulation which changes the results. I don't know how much of this you have changed but I think it's good to know a lot of things can influence your results.