It's not really an Amex issue, rather a vendor policy that will be stopping the use of the card. As someone said, many vendors do not accept Amex. Just as some will not accept MC and yet might have Visa, etc.
So the issue is with Joanne's. If they choose to do their business that way, that's their choice.
Perhaps this is the first time you've run into this issue, though keep in mind, Joanne's is NOT the only one that will not accept Canadian cards for doing business in the USA. Just as the other poster mentioned their USA card not being accepted here in Canada.