I think it's interesting that Magus can't hurt Lavos right then, but he can later. What changed? Perhaps it was the fact that he had Queen Zeal to leech off of, but you can beat Lavos without destroying the Omen. If, on the other hand, it is true that Lavos was getting pissed off that the Zealians were leeching his power, then he shouldn't have been as strong as normal, and you should have been able to hurt him easily. Either way, something's wrong here.
Perhaps this Black Wind is involved?