It seems the game constantly has my throttle and yaw axis reversed. I've tried inverting them in the setup options, to no avail. I read a topic on some other forum that suggested changing the values in the input.map file manually (swapping "p" for "n") but that also doesn't work. I'm using an x-45 stick. I'm not sure if it's coincidence both axis are on my left controller but needless to say it's pretty hard to fly if half my controls are backwards.

Anyone else experience this?

I had the same problem: I assume you are giving a new name to your SAVE AS: I, of course used "trek." And you have to Save As for each and every save you make. Should say ex. trek.map.

As far as the throttle reverse axis, it worked when I followed this sequence:

1) Check the reverse axis box FIRST. Make sure your slider is in the down postion BEFORE doing this.

2) Then, AFTER checking the box, move the throttle slider from BOTTOM to TOP.

3) Make sure you save as with your own map name.

It worked for me, hope it does for you. Good luck.