Please give a try to the attached NetBeans project.
The LOAD button triggers loading of an fxml where we have a ScrollPane on which hvalue = vvalue = 0.5.
The controller prints these two values just after loading: as expected they're equal to 0.5.

Now we add the ScrollPane to a scenegraph and display the app: the scrollbar are rendered at value 0.
The PRINT button prints current values, which have been reset to 0.