removeElement() and clear() doesn't work in doctrine 2 with array collection property

I'm trying to get some simple CRUD done with doctrine 2 but when it's time to update a record with one property set as an array collection I don't seem to get removeElement() to work as it's supposed to. I even tried doing it in this ridiculously ugly way:

foreach($entity->getCountries() as $c) {
        $entity->getCountries()->removeElement($c);
        $this->em->persist($entity);
        $this->em->flush();
}

and it didn't work... Anyone knows how to handle this? I've asked for a solution to this in many different forms and haven't got a good response so far... seems there's lack of good examples of Doctrine 2 CRUD handling. I'll post more code at request.

Edit

//in user entity
/**
 * 
 * @param \Doctring\Common\Collections\Collection $property
 * @OneToMany(targetEntity="Countries",mappedBy="user", cascade={"persist", "remove"})
 */
private $countries;

//in countries entity
/**
 *
 * @var User
 * @ManyToOne(targetEntity="User", inversedBy="id") 
 * @JoinColumns({
 *  @JoinColumn(name="user_id", referencedColumnName="id")
 * })
 */
private $user;