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eBay calculating inaccurate shipping cost when buyers purchase multiple quantities.

I have been having a lot of problems with how shipping calculates for buyers when they buy multiples of the same item. For instance, I had a quantity of 6 available of one item and shipping was in a padded flat rate envelope. A buyer bought all 6 and eBay charged the buyer for one padded flat rate envelope. That shipping option was for one item, not a quantity of 6. They didn't all fit in one envelope. I ended up spending more in shipping than the buyer paid in shipping costs. I have another item today with a similar issue. I had 3 available in a large box that weighs 20 lbs. When a buyer bought all 3, eBay increased the weight of the box to 60 lbs and only billed for one box with the same dimensions. Because of the size, these 3 items all need to be shipped individually as separate packages, so eBay should have tippled the shipping cost to the buyer. The buyer is across the country so the difference in shipping cost between what eBay calculated and what it costs me is $120. Is there something I'm missing when I create my listings that can resolve this issue or is this just a limitation of the system? Due to the weight of many items I sell and the massive shipping cost disparities based on where in the country a buyer is located, I just can't do free shipping. I need this to be accurate. 

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eBay calculating inaccurate shipping cost when buyers purchase multiple quantities.

This recently has happened to me with a heavy product, 3 were purchased together and I had any additional purchases of the same item to cost the difference that it would cost however the buyer was charged just for the shipping of the one which made my profit fly out the window. I did ship anyways and reached out to ebay about this but ended up just counted that loss. SOLUTION FOR ME... after that I did began to list only one quantity at a time with those products until I decided to just up the shipping for coverage in case that happened again.  

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