If you have 'item ships in original box' checked near bottom of product listing it will calculate x items times x boxes.
Also, CP calculates heights, lengths, and widths one against the other so your box definitions and product definitions need to take this into account... ie: a 10 x 20 x 30 item, plus 30 x 20 x 10 item won't calculate to fit in a box defined as 20 x 20 x 30 (even though the two items will in fact fit a box that size).
Nor will CP calculate a situation where you can pack 3 items in a box with two of the items facing upright and the third on its side.
I created a bunch of theoretical box definitions that will accommodate the various combinations of my articles, even though I don't actually use boxes in all those sizes. But CP charges on a weight/volume basis, so the rates calculates out accurately for me.
And one other thing....CP module allows you to add a handling charge ...you could double check that you've not got some big charge per box added that you don't realize.