What you want to know is:
... If a box is present (current photoeye), is it moving?
OkiePC is spot on for a laser doppler velocimeter, but I'm sure the price kills that idea.
It looks like these boxes are being conveyed on a roller conveyor. What if you remove the drive belt/device for one roller so it becomes an idler roll. Then place a sensing device to detect if that roll is moving or not (thus if the detected box is moving).
Various ways to detect the roll turning like cut some holes in the roll and detect metal/no metal with a prox switch