If one rod is longer than the other, the servo has to turn less to move aileron further. Therefore you will get higher throws on the rod that is the longest.
With the shorter rod, the servo has to move more to push the rod the farthest. So you will end up with different throws when the constant is the travel of the servo.

Check which one is the one with the least throw - is it the one with the shorter rod? It should be.