Considering that they were able to release the last part of season one last fall not too long after we heard about Funimation dropping the distribution rights to Yu-Gi-Oh!, I think that they're still have the distribution rights for that series. Although, I'm not completely sure, but I haven't anything official that says that they aren't able to distribute the series.
As for when they'll release season two and three, that's hard to say. If they do have the rights, I could see them releasing a two-disc set for season two in the fall since GX has had yearly releases for the last three years. If that is the case and they continue to release a set once a year, it would take them a long time to just finish season two, let alone season three. I'm not sure if they would make a full season box set like they did with seasons one through three of DM since GX was never as popular or successful as the first series.
