Internal Reconciliation - some documents not reconciling

Hello,
We've recently begun using the tool: Business Partners -> Internal Reconciliation -> Reconciliation.
We select:
Automatic
All of our Customer Business Partners in the range selection
Matching Rule 1 - Ref.2  (which is ORDR, NumAtCard), which we also include on the Incoming Payment
Document Date - which we set to 60
Each day we run this, and we get several reconciliations, which allows us to send out invoices with "payment received", and a $0.00 balance owing. It shows us the Ref.2 numbers, which match.
However, we have a few each day which do not reconcile, and we have no idea why. We have looked through the marketing documents and everything matches and is within our date range, etc. Even payments which were made immediately by credit card the same day do not reconcile.
Any ideas? Anyone else having this issue?

We have a lot of customers who pay by credit card, which we process with "payment on account". We need to have these reconciled each day so their invoices (receipts) show the payment applied and $0.00 owing.
We were told this was the best way to automatically reconcile by our consultant for SAP.
Any one else?
Thanks in advance,
Christine

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