Hi DHB,
We've been working with Doug to try and track this down, but to date have not been able to duplicate the situation. As you said, it does not happen all the time so that makes things a little more difficult.
Using the current release of Recievables 6.8B and our sample data, I tried doing a pre-payment, an invoice for a slightly larger amount, a zero cash entry to match the pre-payment to the invoice, and a Period to clear transactions to History, and the Aged Trial Balance report showed the correct (small) amount.
There are 2 different ways to enter a pre-payment in Receivables; one is to simply enter the payment amount at the top and not apply it to a particular document, and the other is to click New and type in a future invoice number. Which way do you enter pre-payments? If the latter, do you actually post the invoice with the same document number or use a new one? I tried both methods for the above steps with success.
After period end, take a look at all three transactions for the customer (the pre-payment, the invoice, and the zero cash to match them) - do the current amounts have appropriate and expected values?
Perhaps this situation is related to a very specific sequence that is used during the entry of a transaction, which is why it happens only some of the time.