The spells are affected during the casting (as is the case with most spells.) The way the magic works here, presumably, is that the Orb of Whatever is summoned by the caster, lobbed at somebody, and held together by magic for the duration of the flight (which is less than one round, so they're instantaneous in that they have no mechanical duration). Because it's held together by magic, an orb won't be totally effective inside and AMF...but it's still a ball of acid hurtling towards your face, so it's going to hurt a bit.