Magento – Paypal Pro Instant Payment Notifications

When Check/MO method is used, the invoice is created post checkout once you've received funds for an order. There is a checkbox letting you decide whether or not to send the invoice emails when you create these invoices.

When the PayPal method is used and configured to use the "Sale" mode, these invoices are created at the same time as the order is placed because the customer is being charged upon order placement vs fulfillment. I.e. The credit cards are being both authorized and funds captured in a single transaction.

Magento does not send invoice emails (for any payment method) when a Sale/Auth & Capture mode is being used. If you were to switch to the Authorize mode, it would function pretty much the same as the Check/MO method in that you would have emails sent for invoices and also would have to create them upon fulfillment to actually capture the payment.

If your URL is correct then it's what Keyur Shah already commented, but probably wasn't clear enough. If you have IPN enabled and receive payments from different sources (ebay, Magento and others) to the same PayPal account, PayPal unfortunately continues to try sending notifications related to these order to the Magento store, where these orders don't exist.

A possible solution is creating a centralized IPN reciever, see this URL for a very useful script to get you started. http://codeseekah.com/2012/02/11/how-to-setup-multiple-ipn-receivers-in-paypal/