As far as I remember, if you have 3 atmas active and then remove and add different ones it will then only remember the ones you added, so perhaps you had 2 different Atmas + Apoc, changed the 2 atmas to RR + GH and now it only remembers those. If, next time you enter Abyssea you manually select the 3 Atmas, it should remember that congifuration in future.