Additional payment module and transaction information would also be useful. Where did the module come from (builtin or provide link)? The configuration for the payment module used? Was the module removed and reinstalled / configured after the upgrade? Was a "callback" such as IPN involved (can check the server access logs around the time of the order)? Did the customer actually press the button twice (can check the server access logs around the time of the order)? Any modifications to the default checkout process?
Maybe another can chime in (I've not worked directly with the PayPal Pro code), but I remember reading somewhere while PayPal Pro does not require IPN, it will accept IPN calls from PayPal to update the order (such as cost adjustments, refunds, etc)...


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