When the game resolution is set lower than the monitor's native resolution, transitioning between the main screen, designer, and into flight will cause it to reset to the monitor's native resolution. The settings show the resolution as the monitor's native, but it still thinks the game is displaying at the selected resolution, as trying to reselect it causes nothing to change.
This is similar to this bug report, but I am not 100% sure if it is the same issue and I may have explained it better.
This post has been merged with this post.