I believe it had something to do with the restructuring of the website or something. I had a few games registered under my name back when I first got them. Then several months later, the site was very different than it had been before. And the games I had already registered were no longer there. I tried re-registering them, but I had the same problem as you did and couldn't because it was a different input system.

Unfortunately, I don't think there is anything you can do to change it. You could try contacting Square Enix's support staff for more information. But I don't think they can retroactively register your game for you.