Do you have package preferences and do you have a fee on the boxes you have listed in package preferences?
A fee attached to the shipping profile will be added for each item. A fee on your boxes or envelopes in package preferences will be added once per box.
If you have a fee both places, then both will be added.
If you click on the receipt number of your order - that next page will break down for you what was charged.
Shipping
Handling
Packaging