Doctrine 2.4.6 update problem

Maybe I have stumbled into a strange problem. This repo may be used to reproduce it.

Database setup

Please insert your connection settings at em.php then create the tables:

USE test;

CREATE TABLE `usuarios` (
  `id` int(11) NOT NULL AUTO_INCREMENT,
  `usuario_nome` varchar(100) NOT NULL,
  PRIMARY KEY (`id`)
) ENGINE=InnoDB DEFAULT CHARSET=utf8;

CREATE TABLE `orgs` (
  `id` int(11) NOT NULL AUTO_INCREMENT,
  `usuario_id` int(11) NOT NULL,
  `nome` varchar(100) NOT NULL,
  PRIMARY KEY (`id`),
  KEY `usuario_id` (`usuario_id`)
) ENGINE=InnoDB DEFAULT CHARSET=utf8;

CREATE TABLE `admins` (
  `id` int(11) NOT NULL AUTO_INCREMENT,
  `empresa_id` int(11) NOT NULL,
  `usuario_id` int(11) NOT NULL,
  `created_at` datetime NOT NULL,
  PRIMARY KEY (`id`),
  KEY `usuario_id` (`usuario_id`),
  KEY `empresa_id` (`empresa_id`)
) ENGINE=InnoDB DEFAULT CHARSET=utf8;

INSERT INTO `usuarios` VALUES (1,'One'),(2,'Two');
INSERT INTO `orgs` VALUES (1,1,'Company 1');
INSERT INTO `admins` VALUES (1,1,1,'2014-10-01 00:00:00'),(2,1,2,'2014-10-23 00:00:00');

Running

composer install
php index.php

After running index.php you'll see that Doctrine hasnt updated the database records.

Now if we comment line 56 of Organization.php the UPDATE executes correctly.