American Express extract - Bank Statement Reconciliation ?

I'm just reviewing a new business process request and wondering if anyone has ever built this type of interface before ?

I have been tasked with automatically reconciling the American express bank statement line with the system transactions. Seems simple enough, but American express deduct the card transactions fee at source, meaning the amount returned on the bank statement does not reflect the amount we have requested to collect. Therefore the bank statement amount and system transaction amount are out of balance. There is also the possibility that the difference includes both transaction fee and possible charge back amount for failed collections, so I need to be able to analyse the balance difference to ensure it is allocated correctly.