Hey Wayne, does the payment show up anywhere in transactions? I'd be happy to get online with you and the customer to see if I can help you. The area of the code where it actually applies the payment to the invoice is standard Sage, not specific to APS, but we might be able to figure it out, if you'd like.
Can you tell if there's anything different about that invoice? Is it possible that there are two similar-looking invoices? I'm just taking wild-a** guesses because I've not seen this happen before. Just let me know if you want us to take a look.