Linking (re-linking) o/m2m relations with array of ids in Doctrine_Record fromArray stopped working

class User extends Doctrine_Record
{
	public function setTableDefinition()
	{
		$this->hasColumn('username', 'string', 64, array('notnull' => true));
		$this->hasColumn('password', 'string', 128, array('notnull' => true));
	}
	
	public function setUp()
	{
		$this->hasMany('Role as Roles', array('local' => 'id_user', 'foreign' => 'id_role', 'refClass' => 'UserRole'));
		$this->actAs('SoftDelete');
	}
}

class Role extends Doctrine_Record
{
	public function setTableDefinition()
	{
		$this->hasColumn('name', 'string', 64);
	}
	
	public function setUp()
	{
		$this->hasMany('User as Users', array('local' => 'id_role', 'foreign' => 'id_user', 'refClass' => 'UserRole'));
	}
}

class UserRole extends Doctrine_Record
{
	public function setTableDefinition()
	{
		$this->hasColumn('id_user', 'integer', null, array('primary' => true));
		$this->hasColumn('id_role', 'integer', null, array('primary' => true));
	}
	
	public function setUp()
	{
		$this->hasOne('User', array('local' => 'id_user', 'foreign' => 'id', 'onDelete' => 'CASCADE'));
		$this->hasOne('Role', array('local' => 'id_role', 'foreign' => 'id', 'onDelete' => 'CASCADE'));
	}
}


$role = new Role();
$role->name = 'publisher';
$role->save();

$role = new Role();
$role->name = 'reviewer';
$role->save();

$role = new Role();
$role->name = 'mod';
$role->save();

$user = new User();
$user->fromArray(array(
	'username' => 'test',
	'password' => 'test',
	'Roles' => array(1, 2, 3),
));
$user->save();

//--------------------- here goes the failure
$user->fromArray(array(
	'Roles' => array(1, 3),
));
$user->save();

After a User is saved once with some roles, it cannot be saved here with another combination of roles, consisting of some roles which was saved to the User before.
In short, ->unlink() in fromArray method does not schedule a deletion of old relations before adding new ones on save, like it was in previous versions of Doctrine.
Hence the primary key constraint is violated and the exception is thrown:

SQLSTATE[23000]: Integrity constraint violation: 1062 Duplicate entry '2-1' for key 1
#0 D:\projekty\cms-trunk\cms\library\Doctrine\Doctrine\Connection\Statement.php(269): Doctrine_Connection->rethrowException(Object(PDOException), Object(Doctrine_Connection_Statement))
#1 (...)\library\Doctrine\Doctrine\Connection.php(1032): Doctrine_Connection_Statement->execute(Array)
#2 (...)\library\Doctrine\Doctrine\Connection.php(677): Doctrine_Connection->exec('INSERT INTO `us...', Array)
#3 (...)\library\Doctrine\Doctrine\Connection\UnitOfWork.php(631): Doctrine_Connection->insert(Object(Doctrine_Table), Array)
#4 (...)\library\Doctrine\Doctrine\Connection\UnitOfWork.php(562): Doctrine_Connection_UnitOfWork->processSingleInsert(Object(UserRole))
#5 (...)\library\Doctrine\Doctrine\Connection\UnitOfWork.php(81): Doctrine_Connection_UnitOfWork->insert(Object(UserRole))
#6 (...)\library\Doctrine\Doctrine\Connection\UnitOfWork.php(452): Doctrine_Connection_UnitOfWork->saveGraph(Object(UserRole))
#7 (...)\library\Doctrine\Doctrine\Connection\UnitOfWork.php(137): Doctrine_Connection_UnitOfWork->saveAssociations(Object(User))
#8 (...)\library\Doctrine\Doctrine\Record.php(1690): Doctrine_Connection_UnitOfWork->saveGraph(Object(User))
#9 (...)\test3.php(124): Doctrine_Record->save()
#10