Naturally they're going to change. You have one servo in the aileron channel and one in the flap channel with a flaperon mix on. There is only one end point on each.

Go to flaperons, hold full up elevator and set them even. Usually, I have to cut the large one down. Then go to full down elevator and set those end points. When you use ailerons, you should have the same travel on both sides.

I use JR, but fly a buddy's Eclipse every weekend (he doesn't fly his scale planes any more. I think they adjust the same, or close to it.

If you are wanting less flaperon throw on both, you need to cut down the percentage of flap mix, not the end point. I normally set my end points to 150% and dual rates to 125% (max on both) for starters, the set low rate and expo. I set the flaperon end points at this full throw, then later go back and reduce the mix percentage to what feels right.