Pacification doesn't "interrupt" cast bars. The cast bar will go through and finish anyways, if the pacification buff is still up when the bar is done, the skill won't happen. Maybe that's what you're experiencing.

Magical attacks are the regular spells that THM and ACN have. Almost everything else is a weaponskill. You have to time it so the pacification debuff is up at the end of the cast bar so the weaponskill doesn't happen. Otherwise you're better off stunning/dodging.