Paypal transactions not completing.

[DrByte]

It is the ipn_main_handler.php file that is producing both these outputs

Yes, it is. And the IPNs are merely indicators that a transaction happened at PayPal, and PayPal is notifying the store.

The problem is that the store doesn't have record of the order, and the IPN handler is merely confirming the same fact that the OP posted initially.

which suggests (to me) that there is a data/version mismatch between this file and the /module/payment/paypal* file(s).

Can you explain how you came to that conclusion?



I think the real problem here is that something is happening in the store's checkout operations, AFTER the PayPal steps occur, and that "something" is causing the PHP code to abort before the data is saved and emails are sent, etc.
Tests I'd do include going through a full checkout purchase and seeing what exactly does happen, as far as the customer sees.
And also, turn on the PayPal debug logging, and look at (and post) the PayPal_xxxxxx.log files for the specific transaction, not the ipn_xxxxx.log files.