My guess is that it's something with the joystick drivers on your particular setup that is doing something unusual. You should only have to calibrate once, and once that works, the simulator remembers the settings and they will be exactly the same the next time you start up the sim. If the behavior is different at different start-ups it must mean that the output (from your radio via the operating system) changes somehow. (Either that, or that your operating system somehow keeps Freerider from actually saving the settings. On Linux, they can be found in ~/.config/unity3d/[CompanyName]/[ProductName] I believe, so you can check if they are kept correctly).
You should know that I have spent a lot of time working with the calibration to enable it to work with most operating systems and USB controllers/dongles/radios. There are so many different variables, and some devices that give very strange values. I am developing in Unity and am using Unity's input manager the best way I can.