Unexpected behavior while using association on a non primary key field

Entities\Payment:
  type: entity
  table: payments
  fields:
    id: 
      id: true
      type: integer
      nullable: false
      generator:
        strategy: IDENTITY
[-- skipped --]
  manyToOne:
    order:
      targetEntity: Entities\Order
      inversedBy: payments
      joinColumn:
        name: scode
        referencedColumnName: scode

Entities\Order:
  type: entity
  table: h_orders
  fields:
    id:
      id: true
      type: integer
      unsigned: false
      nullable: false
      generator:
        strategy: IDENTITY
    scode:
      type: integer
      unsigned: false
      nullable: false
[-- skipped --]
  oneToMany:
    payments:
      targetEntity: Entities\Payment
      mappedBy: order

$payment = new \Entities\Payment();
...
$order = $this->em->getRepository('\Entities\Order')->find(46320);
$payment->setOrder($order);
$order->addPayments($payment);
$this->em->persist($payment);
$this->em->flush();