If your question is not one of the top 30 questions that can be answered with a script, eBay customer service is pointless ... and often misleading. Obviously, flat rate postage cannot be put on a box.
It is possible that you are using the mobile interface rather than the computer interface for shipping, but if you were using the computer interface I would assume that the radio button at the top is set to "Carrier Packages", and needs to be switched to "Custom Size". This will then allow you to view and purchase postage options for a box rather than USPS flat rate.
