Is anyone having real time shipping problems calculating correct costs?

[TwoDumbDames]

Most of our items are sold by weight. I have an order for 39 lbs of candy. The customer was charged 18.96 and the cost when I go to print the label is more than double that amount. I was online with help yesterday for almost 2 hours and never got any resolution to the problem. They said it was my box size and that all calculation are for the box size not the weight. My site has been set up for 5 years and we have never had this problem until their new version. I'm at a losses to what to do. At this point I am losing money on almost every shipment. 

We have hundred of items that range from 1/8th pound up to 2 pounds. I have no idea how much or how many items someone is going order so box size calculations do not work for us.

Any Help would be much appreciated during the busiest shipping time of our year.