This is because Tyvok has made a custom homing procedure in their controller that has to be ran from the LCD. Since there is no Y limit switch on the machine, they call Y’s current position ‘Home’ for Y, then will seek home out with the X axis.
Unfortunately, there is no way to do this from Lightburn. You must home the machine manually from the home button on the LCD. After that, the machine will act as you expect and run jobs properly.