We ended up offering free shipping to a bunch of disgruntled customers.
There are actually bitcoin users out there who aren't up-to-date on how long it takes to process a transaction?
Happened to me a few weeks ago - I tried to buy something and it got confirmed, but not fast enough for Bitpay, and they cancelled the transaction. So I was out the fees both ways. It was unpleasant, but not surprising, given how shoddy the whole system is.
Everything is fees with Bitcoin - fees for transactions, fees for exchanges, fees for mining pools, dev fees for mining applications, etc. There are no end of middlemen, and they all have their hand out. Sure, each of them is providing some legitimate service, but it sure makes 3% merchant fees for Visa look positively cheap in comparison. And did I mention the instant transaction times, the fraud protection, and the complimentary hardware token that's accepted by millions of businesses worldwide!? Try a credit card today!
Regardless of the answer, variable and large fees really do make this sort of transaction a minefield.