I have bought open box items from Best Buy. I got a 32 GB iPad Mini in January for $409. Assuming this is the same store, it is probably due to the condition or missing items/box condition as was mentioned.
Pricing for each item is set by the store, so call that store to find out why the difference.
I find this to be a great way to save on products that are "never on sale", like Apple. I was checking their website everyday last month for a 13" rMBP when there was a 10% off open box items coupon. That $1,599 device goes for ~$1,385 when it is there. My local BB has a 256 GB 13" MBA, the new one, for $1,164.99 right now. I probably won't pull the trigger on it, as I'm still hopefully for a Haswell rMBP this year, and I would do better with an educational discount at Apple. (Although I've heard BB has and edu. discount, but I don't see it advertised.)