Hi,
Well, if the order status had already been changed manually, this could indicate that the payment was authorized but not captured immediately. And thus the payment notification would have arrived later on, either if the merchant had to manually confirm the payment on his PayPal merchant account, or if PayPal had a delay to validate the payment (it can happen for payments made not with a credit card or the PayPal account's balance, but with an echeck or a bank transfer (through paypal). In that case, several days can separate the payment and the validation of the payment and thus the notification happens only several days later, at which point the merchant might have already manually confirmed the order.