I am having the same problem, but I am dealing with large invoices that apply to multiple customers.

I manually split the incoming payments among the correct customers. When you do that, however, Quickbooks does NOT allow you to match the payment to the invoice - and vice versa (if I Match I cannot also Split).

So, my process is:

- Split the payments to the correct customers

- Then I have to go to 'Invoices' and mark them as paid.

Could that be the reason why they are still showing as A/R? Also, how do you correct the problem without going back and Matching?