This is just a personal opinion, because I don't think its ever actually explained, but I think in Future Rachel's version of events Melissa was part of the team and Ax never was. I get this from the MM where the timeline is all screwed up and Melissa is there instead of Rachel. Just an idea.
But no, they never specify. Because, as the Ellimist says, every decision and every action changes the future.
EDIT: Another option: In this alternate version of the Aniverse Ax is never rescued, but the David situation still occurs and he's the one who sells the Ani's out resulting in the final takeover of Earth and the "6 human Animorphs" being captured.