Everything isn't always a conspiracy. Given the cutting edge IT we have to use, there is a pretty high chance this is just some kind of glitch. I recently had an AA ticket to ICN that did not have the discount applied. GT could see that, couldn't fix it and put it in their notification system to get a solution.
You do realize that if you can find a ticket cheaper from another source including going directly through the airline, you can just buy it with your company card, right?