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It is possible that the auto-apply batch did not get released or suspended. Try the following: open the release AR batches screen and see if there is a batch in there with an S status. Another thing to try is to start a payment application batch for $0.00 and select the customer of one of the payments/credit memos, make the document type either payment or credit memo and use F3 on the document number field to see if that payment or credit memo shows. If it does, select it and see if you get a message that the payment or credit memo is already applied in a different batch number. If so, that will tell you the batch that did not fully release. If no message, it sure sounds like the auto-apply never happened.
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