Run this test app :

"

import javafx.application.Application;
import static javafx.application.Application.launch;
import javafx.beans.value.ChangeListener;
import javafx.beans.value.ObservableValue;
import javafx.scene.Scene;
import javafx.scene.control.TextArea;
import javafx.scene.layout.HBox;
import javafx.stage.Stage;

public class testTextArea extends Application {

    public static void main(String[] args) {
        launch(args);
    }

    @Override
    public void start(Stage primaryStage) throws Exception {
        StringBuilder string = new StringBuilder();
        for (int i = 0; i < 5000; ++i) {
            string.append("This is a very long text in order to test something.").append(i).append("\n");
        }

        HBox box = new HBox();

        Scene scene = new Scene(box);
        primaryStage.setScene(scene);
        primaryStage.show();

        TextArea textArea = new TextArea(string.toString());

        box.getChildren().add(textArea);
        textArea.scrollTopProperty().addListener(new ChangeListener<Number>() {

            @Override
            public void changed(ObservableValue<? extends Number> observable, Number oldValue, Number newValue) {
                System.out.println(newValue);
            }
        });
        textArea.setScrollTop(1000);
    }
}
"

You will see that the call to setScrollTop is not working because the method "scrollBoundsToVisible" in TextAreaSkin is being called afterwards setting a new scrollTop value to 0.