Marketpress over charging shipping

Hi. we are getting grief from a client that is telling us that every order that is shipped via ups is overcharging the customer. We have tweaked the box sizes and weights and it looks like each order is about 18.5% higher to the customer than the actual charges from ups. They have gone to UPS to complain and their rep is telling them that the plugin is no good and that the box sizes are messing with the charges. Is there anything else I can do or even tell them that will help with this? The only other thing I can think of is to lower the product weights below actual and tweak that until the shipping is close. They have over 1000 products so that is not very practical. Please advise.