I submitted a ME order/submission this summer, well marked as such. It was delivered, scanned into CGC, but not received for several days. I sent an inquiry into CGC after a week. The issue was the submission form; I had slipped the submission form inside the plastic bag containing the 1st book of the submission. They couldn't find the form in the box/bag, but eventually created it based on the package tracking number.
I would push CGC on this, as it doesn't make sense that they would process your Standard submission, and not the Walkthrough if they were in the same package.