I wonder if the tour agency through which you bought the tix is part of the problem -- perhaps you were on a lower fare than you realize. Booking classes X I O R N T and E on Air China don't earn any mileage, contrary to post #5 above.

Can't imagine why CA can't see that you took the flight, however...that may just be the boilerplate miles refusal letter that no one bothers (or has the English) to edit. Or perhaps the travel agency buys a block of ticket numbers without assigning pax names until later, and that's all your CA contact has access to. Shouldn't be that way, but maybe the travel agency has experience with this, and/or a contact at the airline that could assist you.