JavaScript2Java Bridge arrays do not work on Linux.
Try the following example to reproduce that:

import com.sun.webpane.webkit.JSObject;
import javafx.application.Application;
import javafx.scene.Scene;
import javafx.scene.web.WebEngine;
import javafx.scene.web.WebView;
import javafx.stage.Stage;

/**
 *
 * @author javafx
 */
public class JavaFXApplication1 extends Application {

    /**
     * @param args the command line arguments
     */
    public static void main(String[] args) {
        launch(args);
    }
    
    @Override
    public void start(Stage primaryStage) {
        WebView view = new WebView();
        WebEngine e = view.getEngine();
        int []array = new int[3];
        array[0] = 42;
        JSObject window = (JSObject) e.executeScript("window;");
        window.setMember("test", array);
        Object o1 = e.executeScript("test[0];");
        Object o2 = e.executeScript("test.length;");
        System.out.println(o1); // Expecting "42"
        System.out.println(o2); // Expecting "3"
        primaryStage.setScene(new Scene(view));
        primaryStage.show();
    }
}

The following output is generated:
Exception in thread "JavaFX Application Thread" java.lang.NoSuchMethodError: booleanValue
undefined
undefined
at com.sun.webpane.webkit.JSObject.setMemberImpl(Native Method)
at com.sun.webpane.webkit.JSObject.setMember(JSObject.java:37)
at javaapplication1.JavaFXApplication1.start(JavaFXApplication1.java:30)
at com.sun.javafx.application.LauncherImpl$5.run(LauncherImpl.java:319)
at com.sun.javafx.application.PlatformImpl$5.run(PlatformImpl.java:206)
at com.sun.javafx.application.PlatformImpl$4.run(PlatformImpl.java:173)
at com.sun.glass.ui.InvokeLaterDispatcher$Future.run(InvokeLaterDispatcher.java:76)
at com.sun.glass.ui.gtk.GtkApplication._runLoop(Native Method)
at com.sun.glass.ui.gtk.GtkApplication$3$1.run(GtkApplication.java:82)
at java.lang.Thread.run(Thread.java:722)

Some other of our JS2Java tests which previously failed due to different reasons also fail with this exception, so the problem might be wider then JS2Java array.