When you have a customer buy mulitples of the same item and have additional shipping charges set they only get charged shipping for 1 of them.
I have this happening and contacted ebay, here was there response....
___________________________
I can certainly understand some of the frustration in this matter and
would be happy to assist you with your concerns today. We are sorry this
is currently a bug we are working on to get the additional shipping
fixed to show again on the invoice. What you will need to do is just re
invoice the customer with the correct shipping. Again we are sorry for
the trouble this may have caused you.
I understand your frustration regarding this matter and apologize for
the inconvenience it has caused you.
_______________________________
its kind of hard to reinvoice them when they pay as soon as they made the purchase!!!
) 
