Don't use Priority Mail medium flat rate boxes. I ship over a thousand items PM a year and only lose money shipping 1% of the time or less. You just have to learn the PM system.
USPS priority mail has over a dozen different priced free boxes, envelopes, etc. Prices for Priority Mail shipping is based upon weight and zip code-yours to buyers. Don't estimate, weigh it and use the general PM shipping option at time of listing. (I add 6 oz for the weight of box.) When your item sells, USPS will charge based on your input to buyers zip code. Then, before printing the label, pull down the drop box PM menu to find the best (cheapest) option. About 1/3 of the time, from the Midwest, regional box A or B turns out to be the cheapest way, and saves $. Sellers usually get a discount of 5%-15% from USPS which helps offset ebay/PPal fees on the charged postage.
The trick to PM is the weight. Prices are based between lbs.: 2lbs ships cheaper than 2.1, and stays the same to 3.1, etc. Unless you sell really heavy items, avoid the flat priced boxes-their shipping costs are more expensive for a reason. If you have heavy items, offer FedEx Smartpost (in addition to PM and let buyer choose), which is a FEDEX/USPS joint venture. Takes a little longer, but usually costs less. But you have to drop it off at a FedEx location-they won't pick those up.