Hi,
we tried it here and it seems that everything works as expected. You have to choose one of two m-n directions and set "fetch" property:

after that exported schema will be:
<?php
use Doctrine\ORM\Mapping AS ORM;
/**
* @ORM\Entity
*/
class E2
{
/**
* @ORM\Id
* @ORM\Column(type="integer")
* @ORM\GeneratedValue(strategy="AUTO")
*/
private $id;
/**
* @ORM\ManyToMany(targetEntity="SampleEntity", inversedBy="e2", fetch="EAGER")
* @ORM\JoinTable(
* name="mn",
* joinColumns={@ORM\JoinColumn(name="e2_id", referencedColumnName="id", nullable=false)},
* inverseJoinColumns={@ORM\JoinColumn(name="sample_entity_id", referencedColumnName="id", nullable=false)}
* )
*/
private $sampleEntity;
}
Is this what you need?