I think I've figured out what happened. When I checked out, I added the second item, then when I got to shipment options all
of them showed $0.00, so of course I chose the fastest one - overnight. And later I saw the $10 handling charge.
After your post, I put the same items in my basket again, and this time when I got to shipping options the interface looked a little different, and only the slowest shipping option showed a zero charge. Each of the others showed an increasing charge up to overnight, which was $10.
So it's my fault. I should have disbelieved the pop-up window that told me all the shipping options were $0.00 (too good to be true), and played with the shipping options until I found one where the "handling" charge was zero as well.
Silly me for thinking Gamestop wouldn't have a gotcha in there to deceive and ensnare the unwary.
I have ordered from GameStop online with various free shipping options many, many times now (including an order in the current sale with the free shipping on two or more items offer), and I've never seen this happen. Are you sure that you didn't select some other weird option, or expedited shipping, or something like that at some point while placing your order?