If you find your AA stop working mid battle, make sure you're within range and hit any action. Even if you can't use the action, you will start AA again.

For instance, when I play GLA I tends to press Rise Shield when get in range from passive mode, and my character will start AA. The reason why I press Shield, is because after getting hit they will retaliate and well, they hit my shield, I block, Phalanx time.