Look at the attached movie. When scrollTo is called, ROOT losts its arrow. On the second launch, "item-1" lost its arrow.

What is interesting, I see, that arrows can disappear in different cases:
a) scrollTo call
b) selection (like shift+down) which makes control to do scrolling (a hiden scrollTo call could be there), so, that newly appeared TreeItem has no arrow.

Use this code to reproduce:
(just click button, or select item-1 and click button)

import java.util.logging.Level;
import java.util.logging.Logger;
import javafx.application.Application;
import javafx.application.Platform;
import javafx.beans.property.BooleanProperty;
import javafx.beans.property.SimpleBooleanProperty;
import javafx.event.ActionEvent;
import javafx.event.EventHandler;
import javafx.scene.Scene;
import javafx.scene.control.Button;
import javafx.scene.control.TreeItem;
import javafx.scene.control.TreeView;
import javafx.scene.layout.VBox;
import javafx.stage.Stage;

public class TestTextApp11 extends Application {

    @Override
    public void start(Stage stage) {
        final TreeView tv = new TreeView();
        tv.setPrefWidth(200);
        tv.setPrefHeight(200);
        tv.setRoot(new TreeItem("ROOT"));

        for (int i = 0; i < 6; i++) {
            TreeItem level1Item = new TreeItem("item-" + String.valueOf(i));
            tv.getRoot().getChildren().add(level1Item);
            level1Item.setExpanded(true);
            for (int j = 0; j < 6; j++) {
                TreeItem level2Item = new TreeItem("item-" + String.valueOf(i) + "-" + String.valueOf(j));
                level1Item.getChildren().add(level2Item);
            }
        }

        tv.getRoot().setExpanded(true);

        final BooleanProperty switcher = new SimpleBooleanProperty(true);

        Button b = new Button("scroll");
        b.setOnAction(new EventHandler<ActionEvent>() {
            @Override
            public void handle(ActionEvent event) {
                tv.requestFocus();
                new Thread(new Runnable() {
                    @Override
                    public void run() {
                        for (int i = 0; i < 4; i++) {
                            try {
                                Thread.sleep(500);
                            } catch (InterruptedException ex) {
                                Logger.getLogger(TestTextApp11.class.getName()).log(Level.SEVERE, null, ex);
                            }
                            Platform.runLater(new Runnable() {
                                @Override
                                public void run() {
                                    switcher.set(!switcher.get());
                                    if (switcher.get()) {
                                        tv.scrollTo(-10);
                                    } else {
                                        tv.scrollTo(100);
                                    }
                                }
                            });
                        }
                    }
                }).start();
            }
        });

        VBox vb = new VBox();
        vb.getChildren().addAll(tv, b);

        Scene scene = new Scene(vb, 300, 300);
        stage.setScene(scene);
        stage.show();
    }

    public static void main(String[] args) {
        Application.launch(TestTextApp11.class, args);
    }
}

Affected tests:
ControlsAutomatedTestSuite/javafx/scene/control/test/treeview/TreeViewTest/scrollToTest
ControlsAutomatedTestSuite/javafx/scene/control/test/treeview/TreeViewTest/singleRowSelectionTest
ControlsAutomatedTestSuite/javafx/scene/control/test/treeview/TreeViewTest/multipleRowSelectionTest
ControlsAutomatedTestSuite/javafx/scene/control/test/treeview/TreeViewTest/keyboardShiftUpDownTest
ControlsAutomatedTestSuite/javafx/scene/control/test/treeview/TreeViewTest/keyboardShiftSequentialMultipleSelectionTest
ControlsAutomatedTestSuite/javafx/scene/control/test/treeview/TreeViewTest/keyboardRangeMultipleSelectionTest
ControlsAutomatedTestSuite/javafx/scene/control/test/treeview/TreeViewTest/keyboardHomeEndCycle
ControlsAutomatedTestSuite/javafx/scene/control/test/treeview/TreeViewTest/keyboardCtrlHomeEndTest