Changes of nested embedded collection are not persisted

/**
 * @MappedSuperClass
 */
class container
{
    /** @String */
    protected $tmp = 'ensureSaved';

    /** @EmbedMany(targetDocument="emb", cascade="all", strategy="set") */
    protected $items = array();

    function __construct($items = null) {if($items) $this->items = $items;}
    function getItems() {return $this->items;}
    function getItem($index) {return $this->items[$index];}
    function removeItem($i) {unset($this->items[$i]);}
}

/** @EmbeddedDocument */
class emb extends container
{}

/** @Document(db="tests", collection="tests") */
class doc extends container
{
    /** @Id */
    protected $id;
}

$emb = new emb(array(new emb(), new emb()));
$doc = new doc(array($emb));

$dm->persist($doc);
$dm->flush();
$dm->refresh($doc);

// change nested embedded collection:
$doc->getItem(0)->removeItem(1);
$before = count($doc->getItem(0)->getItems());

$dm->persist($doc);
$dm->flush();
$dm->refresh($doc);

$after = count($doc->getItem(0)->getItems());
var_dump($before); // outputs 1
var_dump($after);  // outputs 2, but expecting 1