You need to fix your timezone settings but that is unrelated to this problem.
To reproduce it, I added the following test temporarily to Doctrine\Tests\ORM\Functional\BasicFunctionalTest.php:
public function testFlushDoesNotIssueUnnecessaryUpdates()
$user = new CmsUser;
$user->name = 'Guilherme';
$user->username = 'gblanco';
$user->status = 'developer';
$address = new CmsAddress;
$address->country = 'Germany';
$address->city = 'Berlin';
$address->zip = '12345';
$address->user = $user;
$user->address = $address;
$query = $this->_em->createQuery('select u, a from Doctrine\Tests\Models\CMS\CmsUser u join u.address a');
$user2 = $query->getSingleResult();
However, since I did not really know how to check that, keeping this test in didnt make much sense.
Can you try this test? Before my patch it issued an UPDATE query but not after my changes.
It is pretty difficult to test this in an isolated manner.