The reason this is happening is because, the relationship order is determined by which user was added first to the system. This is based off the User ID.
For Example: Moms User ID is 1XXXXX. Father is 2XXXXXX. When you add a relationship, if Father gets added first whose user ID is 2XXXXX, and then you add the Mother whose user ID is 1XXXXX. Father will still display second on the relationship order because the mothers user ID begins with a 1.