If the servos have the same center point and the same endpoints, then the difference in how the servos are moving is entirely within the servos. Since no two servos match exactly, this can happen, and is rather common.

One way to work around the problem is to have both elevator channels set to "ELEVATOR" in the transmitter and adjust the AFR curves so that the travel matches as you move the stick. You won't have to change any rates or expo, but the AILEVATOR function won't work or actually be needed in this case, unless you have the elevators working with the ailerons, too.