That is weird. That's at least two instances of the COD mag not zeroing out. But I know it zeroed out with my renewal earlier.
For the record, here's the order in which they scanned the items on my receipt:
Gamer's Club Unlocked pamphlet barcode
Reward Zone card
After those three it lists the 10 issue @Gamer subscription underneath the RZ info and that's zeroed out as well.
So if any of those three are MIA from your receipts, that may be why it didn't package out.
Also the rep had to go into the system and select between the physical or the digital/email version of the magazine sub somewhere within the transaction.