Credit Card Receipt and Invoice Matching questions

Our primary business is wholesale, our finance systems running on
AS400.
We recently generated a Direct To Consumer service, selling items
through our web sites, Infomercials and QVC.
The problem that we are having is in matching some of our credit card
payments to the invoice which is generated when the goods are
shipped. I am sure that other companies don't have this problem, and
it just may be the companies that we are dealing with, but hopefully
someone can suggest a solution.

Orders are raised through the web site (etc), each order being given a
unique Merchant Reference Number on the eCommerce system (all orders
are held here, whether generated through web, phone or QVC).
These are then interfaced to our mainframe system, generating Sales
Orders.

When the items are shipped, the Sales Invoice details (document number
+ amount) are updated on the eCommerce system.

The payment process charges the customer card, updates on the
eCommerce system, and the details are sent to the bank.

The bank itself handles Visa/Mastercard transactions, but passes
American Express and Discovercard sales to those companies.

Eventually (1-3 days later depending on card type) the bank confirms
to us the deposits that were made for the day, however in some cases
our Invoice Number is not shown on the detail file.

90% of the time our Invoice Number does show for Visa/Mastercard,
however for Amex and Discovercard it never shows, and we either get no
reference at all or the same reference for each transaction.

The file from the bank does not contain any other useful reference,
only an Invoice Number, so if this is not in the correct format, all
that we can go on to match with the original sales invoice is the
date, card type and amount.

Is this something that other companies have problems with?
I would have thought that being able to correctly match a payment with
it's invoice, ideally by invoice number (in case of multiple
shipments) or by sales order number (Merchant Reference Number) would
be a standard feature.


2nd complication............

We also have promotions that allow items to be paid in 3 or more
installments. In this case, the payment processing company tell us
that they have to generate a unique reference for each payment, and
this is the only reference we get back from the bank. So in this case
we can't even use amount or date to link back to the original invoice.

Any suggestions on how we might be able to deal with this (other than
switching companies) would be much appreciated.