Example, if you shop at Sears or another company that has both a retail store and catalog to purchase from and they just sold the last blouse you wanted in your size, they could order one from the catolog, but you would have to pay the mailing cost. Think of it on those lines.
If you can wait for her to get more in then that would save you the cost of mailing plus the two extra skeins. If she knows the yarn you need will be included on the list, maybe she would be willing to make a note to set those aside for you when they come in at no extra cost to you. But if you have to have it right away, then yes I understand why she would charge you the mailing cost.
BTW, can this yarn be found on line and can you place an order yourself? It might be cheaper that way if you can.