all good advice, and, indeed, in the above case, I had a print out form American Express showing the seat assignment and had American Airlines on the phone telling JAL that the reservation and seat were confirmed, but JAL insisted that American Airlines, although issuing me a confirmed ticket, did not properly interact with JAL and therefore, they were not obligated to board me. The conflict between the code share selling airline and the code share operating airline is the oddity in this situation and my question is whether others have run into it and how they've dealt with it.