The latest version of JoyToKey works with Crusade as long as the JoyToKey window is focused. So if you're playing Crusade in fullscreen, you can just drag the JoyToKey window to the very edge of the screen so that only the corner of it is overlapping the Crusade window, and click your mouse on it. I don't know why it works, and it won't be important once 0.9.1 comes out anyways.