Your mixing could be a bit off. I had a similar problem with a Futaba set up I had on a plane with elevons. I had to change the percentages in different sections to get the throw to be exactly the same. If i remember right, I had set one of the throws using the chanel output percentage and the other using the mixing percentages and for some resason it affect the throws slightly. When i set the channel percentages to be equal and then adjusted in the mixing section I was eventually able to get the throws identical.