Hi Glen, does the site use the parameter - useimageincart as that will replace the product id however the product id will show on the order in the admin and emails.
Since you're talking about SKUs in the ECT shopping cart software, I'd like to point out that with most manufacturers, the SKU is the Product ID for an item. We use the SKU field in ECT for the UPC number, which is the barcode scan number. This number is also a required number with Google Merchant, so if you have your products up with them, you need it configured in your feed. I've always thought that ECT should change this field to pUPC, it would make more sense.
OK, so, yes, I do have the paramater "usimageincart" turned on, so that explains it. I guess it's just one or the other, but it might be good have a similar parameter to show the ProductID/SKU as well, so that you can show both.