An example to support my answer on StackOverflow: http://stackoverflow.com/questions/7196458/ejb-3-entities-multiple-columns-same-object-reference-problem/7197660#7197660

A.java

package com.stackoverflow.jaizen;

import javax.persistence.Column;
import javax.persistence.Entity;
import javax.persistence.Id;
import javax.persistence.ManyToOne;

@Entity
public class A {
	
	@Id
	private int id;
	
	private String name;
	
	@ManyToOne
	@Column(name = "manager_id")
	private B manager;
	@ManyToOne
	@Column(name = "supervisor_id")
	private B supervisor;
	@ManyToOne
	@Column(name = "worker_id")
	private B worker;
	
	public A(int id, String name) {
		this.id = id;
		this.name = name;
	}
	
	protected A() {}
	
	public String getName() {
		return name;
	}
	
	public void setName(String name) {
		this.name = name;
	}
	
	public B getManager() {
		return manager;
	}
	
	public void setManager(B manager) {
		this.manager = manager;
	}
	
	public B getSupervisor() {
		return supervisor;
	}
	
	public void setSupervisor(B supervisor) {
		this.supervisor = supervisor;
	}
	
	public B getWorker() {
		return worker;
	}
	
	public void setWorker(B worker) {
		this.worker = worker;
	}
	
	public int getId() {
		return id;
	}
	
	@Override
	public int hashCode() {
		return id;
	}
	
	@Override
	public boolean equals(Object that) {
		return (this == that) || ((that instanceof A) && (this.id == ((A) that).id));
	}
	
	@Override
	public String toString() {
		return "A [id=" + id + ", name=" + name + ", manager=" + manager + ", supervisor=" + supervisor + ", worker=" + worker + "]";
	}
	
}

B.java

package com.stackoverflow.jaizen;

import javax.persistence.Entity;
import javax.persistence.Id;

@Entity
public class B {
	
	@Id
	private int id;
	
	private String name;
	
	public B(int id, String name) {
		this.id = id;
		this.name = name;
	}
	
	protected B() {}
	
	public int getId() {
		return id;
	}
	
	public String getName() {
		return name;
	}
	
	public void setName(String name) {
		this.name = name;
	}
	
	@Override
	public int hashCode() {
		return id;
	}
	
	@Override
	public boolean equals(Object that) {
		return (this == that) || ((that instanceof B) && (this.id == ((B) that).id));
	}
	
	@Override
	public String toString() {
		return "B [id=" + id + ", name=" + name + "]";
	}
	
}

JaizenQuestion.java

package com.stackoverflow.jaizen;

import javax.persistence.EntityManager;
import javax.persistence.EntityManagerFactory;
import javax.persistence.Persistence;

public class JaizenQuestion {
	
	private static final int CARMEN_ID = 300;
	private static final int BOB_ID = 200;
	private static final int ALICE_ID = 100;
	private static final int JOB_ID = 9000;
	
	public static void main(String[] args) {
		EntityManagerFactory emf = Persistence.createEntityManagerFactory("sandbox");
		setup(emf);
		change(emf);
		System.out.println("------------------------------------------------------------------------------------------");
		query(emf);
		emf.close();
	}
	
	private static void setup(EntityManagerFactory emf) {
		EntityManager em = emf.createEntityManager();
		em.getTransaction().begin();
		
		B alice = em.merge(new B(ALICE_ID, "Alice"));
		B bob = em.merge(new B(BOB_ID, "Bob"));
		B carmen = em.merge(new B(CARMEN_ID, "Carmen"));
		System.out.println(alice);
		System.out.println(bob);
		System.out.println(carmen);
		
		A job = em.merge(new A(JOB_ID, "The Job"));
		job.setManager(alice);
		job.setSupervisor(alice);
		job.setWorker(alice);
		System.out.println(job);
		
		em.getTransaction().commit();
		em.close();
	}
	
	private static void change(EntityManagerFactory emf) {
		EntityManager em = emf.createEntityManager();
		em.getTransaction().begin();
		
		A job = em.find(A.class, JOB_ID);
		B bob = em.find(B.class, BOB_ID);
		B carmen = em.find(B.class, CARMEN_ID);
		
		job.setSupervisor(bob);
		job.setWorker(carmen);
		
		em.getTransaction().commit();
		em.close();
	}
	
	private static void query(EntityManagerFactory emf) {
		EntityManager em = emf.createEntityManager();
		em.getTransaction().begin();
		
		B alice = em.find(B.class, ALICE_ID);
		B bob = em.find(B.class, BOB_ID);
		B carmen = em.find(B.class, CARMEN_ID);
		System.out.println(alice);
		System.out.println(bob);
		System.out.println(carmen);
		
		A job = em.find(A.class, JOB_ID);
		System.out.println(job);
		
		em.getTransaction().commit();
		em.close();
	}
	
}

output.log

B [id=100, name=Alice]
B [id=200, name=Bob]
B [id=300, name=Carmen]
A [id=9000, name=The Job, manager=B [id=100, name=Alice], supervisor=B [id=100, name=Alice], worker=B [id=100, name=Alice]]
------------------------------------------------------------------------------------------
B [id=100, name=Alice]
B [id=200, name=Bob]
B [id=300, name=Carmen]
A [id=9000, name=The Job, manager=B [id=100, name=Alice], supervisor=B [id=200, name=Bob], worker=B [id=300, name=Carmen]]