Has the charge shown up on your account? I have bought tickets with BA and it has taken weeks for the actual charge to show up. You don't get points until there a charge.
This situation sounds very strange because everything you buy on an amex card earns points, absolutely everything. The only things that don't are cash advance or anything that is treated as a cash advance. I simply can't imagine any agent telling you that purchasing tickets on BA doesn't earn points. There's something that you aren't telling us.