To reproduce run the attached NetBeans project: it loads an FXML file, creates a scene with it, then a stage. You'll see a wrong rendering: the layout is made of AnchorPane > TabPane > Tab > Button but for some reason you get a 5 pixels height window which is empty (attached expected rendering as well as effective one).

As far as I see it's combination of the use of TabPane and the fact root.prefHeight(-1) is called before stage.show() that triggers the issue.
Not calling root.prefHeight(-1) or doing it after stage.show() solves it.
Use another container than TabPane (such as TitledPane) solves it.
Keep TabPane but remove top AnchorPane solves it.