Product Version: NetBeans IDE Dev (Build 200809211401)
Java: 1.6.0

This issue was blogged in http://d.hatena.ne.jp/nowokay/20080827 (But it's Japanese)

It seems that there is a bug in NetBeans debugger that it can not display
object reference properly on Instance View. Please try the following steps.
Actually I'm also seeing the same behavior. Please evaluate.

1. Start NB
2. Create a Java project and prepare the following main class

public class ReferenceSample {
    static class A{}
    static A a = new A();
    static class B{
        A af = a;
    }
    static class C extends B{}
    public static void main(String[] args){
        B b = new B();
        C c = new C();
        System.out.println("" + b + c);
    }
}

3. Set profile point on the following line and set taking heap dump.

        System.out.println("" + b + c);

   http://f.hatena.ne.jp/images/fotolife/n/nowokay/20080828/20080828004111.png

4. Run the project and browse the instance of class A.
   It shows there are 3 references.

   http://f.hatena.ne.jp/images/fotolife/n/nowokay/20080828/20080828004112.png

5. set a break point instead.

   http://f.hatena.ne.jp/images/fotolife/n/nowokay/20080828/20080828004113.png

6. open "Loaded Classes" window in debug window and double click on class A to open "Instance View"

   In References window, it shows only A and B, there is no C reference.

   http://f.hatena.ne.jp/images/fotolife/n/nowokay/20080828/20080828004114.png