UPS Negotiated Rates not Matching up with Worldship

I Think this issue can be fixed in Shipping Charges/Dependencies but I'm not sure how to make that happen. We sell and ship weatherization products, the problem is; for example, on a product page for Fast n Final Spackling 1Qt. tub, on the shipping properties tab, I enter the weight for a single tub, Items in a box, 1 to 6 (6 max to a case/box), Box dimensions for case (6) 11" x 11" x 9". The problem is when someone orders 3 tubs, that will get packed in a smaller box but the shipping gets calculated with the case box dimensions and I'm thinking that what's throwing the shipping rate off, compared to what shipping dept. gets on their scale with Worldship. Anyone have any idea as to a workaround for this?

Thank You!!