I believe it's one redemption per receipt. So you'd get credit just for the one box. But I just got back from Target where I bought two Fancy Feast Petites, so I'll let you know how I'm credited.
If you look at the Shopkick Rules (open app--> click on person icon in top left--> click on gear in top right--> down the bottom you'll see Shopkick Rules) I don't see that it states this rule one way or the other. It does note that you may only submit 1 receipt per merchant per day. So you could, in theory, buy a box of Cheerios at five different grocery stores in one day, and still be within the rules, but you couldn't do five separate transactions at one grocery store. Although there are some DPs in this thread and elsewhere (if you search Shopkick up top here there are a few SK threads) where people have mentioned that SK can be picky about what they perceive to be rule violations.
ETA: can confirm that I was only credited for one.
