Chiming in as well - when this issue comes up, it's usually because the items in question are mapped to a box with a low maximum weight. If you tend to get orders for shipping that have multiple items, map the item to a box with a higher maximum weight (or increase the max weight of the box that is already mapped). This will let the shipping carrier know that multiple items will be packed in the same box, and, avoid the issue of charging for shipping as if you're shipping every item in its own box.
