Anyone ever reconciled their Amazon transaction reports vs what they've actually shipped?

We always reconcile our Amazon sales with our EPOS system every 2 weeks using the payment report by transaction for each settlement period; waiting until the period is closed before printing. Until recently, we have not had any issues with our stock levels, but I checked some of our fast moving lines this week and discovered some serious anomalies.

When I search for sales by SKU for example, it showed 116 transactions for a particular product and after trawling through the list cancelling out returns and adding in multiple orders we had sold 132 of this item. Compare this with the total number of this item sold from the settlement period reports and this is 124. Results are more worrying on faster moving lines, and I am trying to put a case together before I approach Amazon with the problem but wondered whether anyone else had similar experiences, and if so how they went about getting them resolved.