Actually this is nothing to do with the Slingboxes. I assume you see the same effect when you use the real remote ?
The Zaptor boxes will both be using the same IR Codes so each time you transmit an IR Burst from either a real remote or one of the Slingboxes, both the Zaptor boxes will react. Some manufactures (DirecTV, Dish, Tivo...) allow you to have different Remote Addresses so you can operate multiple devices in the same room, but I don't think Motorola have that option. The only solution is to use a cardboard tube/duct tape/metal foil... to isolate the IR Blaster in front of each of the boxes so they only point at the IR Receiver.