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.

[Candlestore]

@TwoDumbDames ;

I do not have a Square Website, but I run into the same issue.  If someone buys one wax melt for $3.99 from me, the shipping is usally about $8 actual.  But since a wax melt fits in small boxes, which are under the minimum shipping size, I have a few choices charge actual shipping (based on size and weight of item), add a shipping markup, Take a loss, or loose the sale.  At least with me the shipping usually encludes a candle which fits in the minimum shipping size so shipping gets closer to actual shipping cost.  But with Shipping costs always increasing its hard to get the exact shipping price.  If you measure the Item and put it in a Box its one rate to ship, someone buys 4 candles it goes in a different box and weight, so the charge per Item shipping of 1 candle is actually higher than shipping 4 candles.  1 Candle to ship might be $7.75, but 4 candles to the same address in 1 larger box might be around $10 to zone 1 from me.  But if I ship to zone 8 from me its over $23 for 1 candle.  So the best way I know how to do this is make your item a little higher in price and include shipping, or measure and weigh your most common shipments and figure out the shipping costs.  I have noticed with my shipping, it gives me a Rate of say $40 for 12 candles to ship.  I go to my shipping calculator, put all 12 candles in a box with padding it fits in and the cost is about $40, but if i ship 6 candles in 2 boxes, shipping might be half that total cost for 2 boxes.  Found a Surge charge for packages over X inches and another Surge charge for over X weight.  

This is how I see people charging $25 for a 16oz candle and I am only chaging about $20 per 28oz candle.  They have shipping included in their price to offer Free Shipping.  Shipping costs have too many variables to get an exact cost especially when people add more than 1 item, no matter what website service you host through.