This is caused by taking the join column name as the identifier while generating a property name for annotation. The mapping driver detects that the same property is already defined and ends the convert process. A little bit smarter approach for me was to take the local table name. But this assumes a specific style of join table naming convention.

Doctrine\ORM\Mapping\Driver\DatabaseDriver::loadMetadataForClass()

Replace:

$associationMapping['fieldName'] = Inflector::camelize(str_replace('_id', '', strtolower(current($otherFk->getColumns()))));

With:

$name = explode("_",$myFk->getLocalTableName());
if (count($name) > 1)
{
array_shift($name);
}
$name = implode("_", $name);

$associationMapping['fieldName'] = Inflector::camelize(str_replace('_id', '', strtolower($name)));

Maybe to switch to this behavior with an additional option?