I too only offer combined shipping with a single payment. Fortunately most times my buyers wait for my invoice before paying. When they DO make multiple payments I send an email and tell them that if they want the Combined S&H charge they must make one payment and offer to refund the multiple payments if they will send one payment.
The key to refunding is that you use the "REFUND" option in Paypal. If you do that you can make a Full or Partial Refund without it costing anyone money. Your customer doesn't get that .30 charge as they would if you send them money AND you get the fee that Paypal charged you refunded (or a percent as applicable). Again you have to use the "REFUND" option (it is at the bottom of the details page I believe) and if you just "SEND" money back then your customer is charged and you don't get your fee back that Paypal charged you.
I use this refund feature a lot, since I try to charge postage + a small handling charge and I sometimes over estimate the weight of a package when listing. If that happenes and the difference is more than $1.00 then I refund the excess.