score:2
Aside from the usual caveats, it's quite possible that your company travel agent has a corporate deal with JL or access to other fares that are not available to the general public. Airlines are free to sell their products through private channels and they retain almost total control over who sells their fares and at what price. This is what we mean when we talk of "private fares" or "corporate fares".
A number of major travel agents (such as American Express travel and Carlson Wagonlit) obtain fares at a significant discount to the public fares. They usually pocket the difference but, with the airline's permission, they may offer some seats at a lower price onto their customers. Major customers will also get large rebates from the airlines that reduce the effective ticket price per person: several major financial houses in London pay less than half what you or I pay for a transatlantic business class fare, although that won't appear on the receipt.
It's also worth saying that JAL uses a slightly strange in-house computer system to manage their fares and flight availability information, and it is interfaced with the rest of the world in an incomplete and slightly unreliable way. (For instance they do not even expose every available booking class on domestic flights to the travel agent systems.) A human travel agent might have more luck in getting their system to work than a website backend would.
Upvote:1
The available seats within a fare class on a specific day can change without notice. If a flight is not selling well on a certain date, they may shift some seat inventory to a lower fare class to fill that flight. If a flight is selling quickly, they may move seat inventory out of the cheap fare class into a higher one. So it is possible that seat inventory changed between when you looked on Expedia and when your TA looked on their system.
According to JAL's US website, both X and D fare classes allow advance seat selection and both seem refundable after a stiff penalty fee. Can't find the same info on their Japan website. http://www.ar.jal.com/arl/region/en/flight_planning/index03.html