I initially thought something similar. When I checked the weights, I saw that the item weights in the store database were 1-2 pounds higher than the actual shipping weight. Also, the boxes are well within UPS requirements, before dimensional charges are applied for UPS shipping.
Also, the differences are very significant. For a 5-pound order (that fits in a 7 x 7 x 12 box), the look-up via PowerStore came up with $8.04 for shipping, whereas the actual UPS charge was $14.97. That is roughly 80% over. A huge difference, and typical of the discrepancies that the customer is screaming at me about.
Is it possible an error on what is being fed to the rate look-up? Or some other back-end calculation? I've run several different test orders and the discrepancy seems for be in the 65-85% range of charged shipping vs. actual shipping. Also, if I log into customer's UPS account online and do a shipping calculation, they match the *actual* shipping charges that are paying.