That happened to me an i found the solution. If u build your project with your .fxml files in different packages from the class that has the launch line
(Parent root = FXMLLoader.load(getClass().getResource("filenamehere.fxml"));
)
and use a relative path your windows except from the first one wont launch when your run the jar. To keep it short place the .fxml file in the same package with the class that launches it and set the path like this ("filenamehere.fxml") and it should work fine.