To reproduce click button "Draw chart" several times.
You will see that series are rendered inconsistently (There is example attached).

import java.util.ArrayList;
import java.util.Iterator;
import java.util.List;
import javafx.application.Application;
import javafx.application.Platform;
import javafx.collections.FXCollections;
import javafx.collections.ObservableList;
import javafx.event.ActionEvent;
import javafx.event.EventHandler;
import javafx.scene.Scene;
import javafx.scene.chart.BarChart;
import javafx.scene.chart.CategoryAxis;
import javafx.scene.chart.NumberAxis;
import javafx.scene.chart.XYChart;
import javafx.scene.chart.XYChart.Series;
import javafx.scene.control.Button;
import javafx.scene.layout.FlowPane;
import javafx.scene.layout.Pane;
import javafx.scene.layout.VBox;
import javafx.stage.Stage;

public class BugBarChart extends Application {

    static int SLOT_WIDTH = 600;
    static int SLOT_HEIGHT = 400;
    static int WND_WIDTH = 800;
    static int WND_HEIGHT = 800;
    BarChart barChart;
    Button changeData;
    Button reset;
    List<XYChart.Data> data;
    Pane buttonsPane;
    Pane contentPane;
    VBox root;
    Button btnDrawChart;
    Runnable action;
    Runnable changeSeries;

    @Override
    public void start(Stage primaryStage) {
        data = getData();

        changeSeries = new Runnable() {
            @Override
            public void run() {
                if (barChart == null) {
                    return;
                }
                
                int overall_counter = 0;
                barChart.setAnimated(true);
                end:
                for (Iterator<Series> it = barChart.getData().iterator(); it.hasNext();) {
                    Series series = it.next();
                    int size = series.getData().size();
                    for (int i = 0; i < size / 2; i++) {
                        if (overall_counter >= data.size()) {
                            break end;
                        }
                        series.getData().set(i * 2 + 1, data.get(overall_counter++));
                    }
                }
            }
        };

        action = new Runnable() {
            @Override
            public void run() {
                Platform.runLater(new Runnable() {
                    @Override
                    public void run() {
                        contentPane.getChildren().clear();
                        barChart = getBarChart();
                        contentPane.getChildren().add(barChart);

                        Platform.runLater(changeSeries);
                    }
                });
            }
        };

        btnDrawChart = new Button("Draw chart");
        btnDrawChart.setOnAction(new EventHandler<ActionEvent>() {
            @Override
            public void handle(ActionEvent t) {
                action.run();
            }
        });

        buttonsPane = new FlowPane();
        buttonsPane.setMaxWidth(WND_WIDTH);
        buttonsPane.setMinWidth(WND_WIDTH);
        buttonsPane.getChildren().add(btnDrawChart);

        contentPane = new Pane();

        root = new VBox();
        root.getChildren().addAll(buttonsPane, contentPane);

        Scene scene = new Scene(root, 800, 600);

        primaryStage.setScene(scene);

        primaryStage.setTitle(System.getProperty("java.runtime.version") + "; " + System.getProperty("javafx.runtime.version"));
        primaryStage.show();
    }

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

    private BarChart getBarChart() {
        CategoryAxis x_axis = new CategoryAxis(FXCollections.<String>observableArrayList("First", "Second", "Third", "Fourth"));
        NumberAxis y_axis = new NumberAxis("Y-Axis", 0.0d, 10.0d, 2.0d);
        Series s1 = new Series(FXCollections.observableArrayList(
                new XYChart.Data("First", 4),
                new XYChart.Data("Second", 5),
                new XYChart.Data("Fourth", 6)));
        s1.setName("Set 1");
        Series s2 = new Series(FXCollections.observableArrayList(
                new XYChart.Data("First", 4),
                new XYChart.Data("Second", 3),
                new XYChart.Data("Fourth", 2)));
        s2.setName("Set 2");
        Series s3 = new Series(FXCollections.observableArrayList(
                new XYChart.Data("First", 4),
                new XYChart.Data("Second", 6),
                new XYChart.Data("Fourth", 8)));
        s3.setName("Set 3");
        ObservableList chartData = FXCollections.observableArrayList(s1, s2, s3);
        BarChart chart = new BarChart(x_axis, y_axis, chartData);
        chart.setMaxSize(SLOT_WIDTH, SLOT_HEIGHT);
        chart.setPrefSize(SLOT_WIDTH, SLOT_HEIGHT);
        chart.setTitle("BarChart");
        chart.setStyle("-fx-border-color: darkgray;");
        return chart;

    }

    private List<XYChart.Data> getData() {
        List<XYChart.Data> series_data = new ArrayList<>();
        series_data.add(new XYChart.Data("Third", 5));
        series_data.add(new XYChart.Data("Third", 8));
        series_data.add(new XYChart.Data("Third", 2));
        return series_data;
    }
}