FULL PRODUCT VERSION :
JDK 9.0.1

A DESCRIPTION OF THE PROBLEM :
JDK-8088731 : CheckBoxTreeItem: must update check state on modifications to children list

issue 3
-check root
-uncheck node 3
-check sub of node 3
-uncheck root

I fixed issue 1 and 3 in my project

I add in CheckBoxTreeItem.updateDownwards()
cbti.setIndeterminate(false);

    private void updateDownwards() {
        // If this node is not a leaf, we also put all
        // children into the same state as this branch
        if (! isLeaf()) {
            for (TreeItem<T> child : getChildren()) {
                if (child instanceof CheckBoxTreeItem) {
                    CheckBoxTreeItem<T> cbti = ((CheckBoxTreeItem<T>) child);
                    cbti.setSelected(isSelected());
                    cbti.setIndeterminate(false); //My fix
                }
            }
        }
    }

maybe it will help.

Sorry for my second letter. But After fixing I have to write for save your time. Thanks


STEPS TO FOLLOW TO REPRODUCE THE PROBLEM :
JDK-8088731 : CheckBoxTreeItem: must update check state on modifications to children list

issue 3
-check root
-uncheck node 3
-check sub of node 3
-uncheck root

EXPECTED VERSUS ACTUAL BEHAVIOR :
EXPECTED -
node is unchecked
ACTUAL -
node is indeterminate

REPRODUCIBILITY :
This bug can be reproduced always.

---------- BEGIN SOURCE ----------
---------- BEGIN SOURCE ----------
import javafx.application.Application;
import javafx.event.ActionEvent;
import javafx.event.EventHandler;
import javafx.geometry.NodeOrientation;
import javafx.scene.Scene;
import javafx.scene.control.*;
import javafx.scene.control.cell.CheckBoxTreeCell;
import javafx.scene.layout.BorderPane;
import javafx.stage.Stage;

public class Test1 extends Application
{
@Override
public void start(Stage stage)
{
Button b = new Button("B1");

CheckBoxTreeItem<String> rootItem = new CheckBoxTreeItem<>("Root Node");
rootItem.setExpanded(true);

final TreeView<String> tree = new TreeView<>(rootItem);
tree.setEditable(true);

tree.setCellFactory(CheckBoxTreeCell.<String>forTreeView());

for (int i = 0; i < 8; i++) {
final CheckBoxTreeItem<String> checkBoxTreeItem = new CheckBoxTreeItem<>("Node" + (i+1));
checkBoxTreeItem.getChildren().add(new CheckBoxTreeItem<>("Sub node" + (i+1)));
checkBoxTreeItem.getChildren().add(new CheckBoxTreeItem<>("Sub node" + (i+1)));
checkBoxTreeItem.getChildren().add(new CheckBoxTreeItem<>("Sub node" + (i+1)));
rootItem.getChildren().add(checkBoxTreeItem);
}

b.setOnAction(new EventHandler<ActionEvent>()
{
@Override
public void handle(ActionEvent e)
{
isSelected(rootItem);
}
});

tree.setRoot(rootItem);
tree.setShowRoot(true);

final BorderPane root = new BorderPane();
root.setCenter(tree);
root.setBottom(b);

final Scene scene = new Scene(root);
scene.setNodeOrientation(NodeOrientation.RIGHT_TO_LEFT);

stage.setScene(scene);
stage.show();
}

private void isSelected(CheckBoxTreeItem<String> root)
{
boolean selected = root.isSelected();

if(selected)
System.out.println(root.getValue());
else
for(TreeItem<String> item : root.getChildren())
isSelected((CheckBoxTreeItem<String>)item);
}
}
---------- END SOURCE ----------
---------- END SOURCE ----------