I hate replying to my own post but
A little more digging around in the database, in the wp_tcp_orders table I see that there is no transaction_id for the orders that came back Pending instead of Completed (For the REAL Paypal transactions, the sandbox ones all have a transaction_id, The comment_internal field is complete for the sandbox, but empty for the REAL PayPal, so now I know where the IPN data is stored.
Should this logging not be enabled for PROD?