I have the same problem when I switch from a higher level job to a lower level job. What happens is that when you switch to the new job, it calculates how many Ability Points you're going to have, and then chops off all the abilities that go beyond it from the end. But usually people have a couple abilities early in the Macro that have lower costs, like an additional basic attack (0 points), Guard (0 points), or Cure/Sacrifice (2 points). So when you try to overwrite that slot with something that takes 3 points, you can't do it because it would end up taking more points than you've got available.

If you select the job Macro, it will tell you that some abilities cost too many points to equiip. But if you go back into your Actions/Abilities Bar, Unequip the last one, then run the Macro again, they should all equip.

Obviously, it would be easier if there was some workaround from the coding side. Like if you try to equip an ability from a Macro, it lops off the last ability from the end of the list. But I don't know anything about coding, so I have no idea how complicated that would be.