Ah... solved my own problem. I think I was getting the wrong EntityManager. I fixed it by getting the EntityManager via the client's container instead of the kernel's one:
public function testFooForm()
{
// ... do some testing
$clientEm = $client->getContainer()->get('doctrine.orm.entity_manager');
$fooRepo = $clientEm->getRepository('CompanyProjectBundle:Foo');
$foos = $fooRepo->retrieveByBar(3);
echo count($foos); // gives the correct result of 2
// ... more happens later
}