Hmmm, I haven't experienced that problem recently or ever. Are you using PayPal? If so, you could refund the overpayment thru PayPal. Are you sending the invoice through eBay or is it the automatic one generated by eBay? Do you want to PM me with your user name and I will look to see if anything looks strange?
Zone 6 at 2 lbs. is $8.60 Priority
Zone 1-2 at 2 lbs. is $5.20 Priority
So let me get this straight, when you print the shipping label and pay for postage, the cost is $5.20 to the address you are shipping to but on the invoice it charges the buyer $8.60? That makes no sense as Priority Mail rates are zoned according to Zip and weight. A buyer paying $5.20 will be within 150 miles of you where a buyer paying $8.60 will be like 800 miles away or so. Who are you using to invoice...ebay or paypal? Who are you using to print the shipping label...ebay, PayPal, or USPS Shipping Assistant? Or some other carrier?
A site with some good, basic shipping information...
http://www.newlifeauctions.com/shipping.html