Ok so your mode is swapped around. Your controller is either in mode 1 or 2 and sim is the other way around. Try making a new controller setup for the game commander and set it up from scratch if you've not already done this. You will have to assighn each channel to each controllable feature. What I am trying to get to is that if your elevator moves with your throttle you have the same channel assighned to them both and you need to go specify one of them differently. In other word you might have assighned the right one to elevator now but you haven't changed the throttle to the right one? Or well it could be the other way around. It's rather simple actually when you take your time to set it up. I always activate the advanced mode and look at the sliders which simulate the movement which each stick input is producing.

In short I take it one small step at a time. Go to the elevators and move my elevator up and down. If they do not move then I know the wrong stick on the radio is assighned to them. Then when I change it I check which of the sliders gets moved by moving the elevator stick and click on it. I like to simplify things for myself and seems like this has worked hassle free.