Zeromus (the blue version) most likely have a Counter-Condition with the following conditions:
- Item #$C8 (Crystal)
- User Class #$10 (Paladin)
- Elemental bit $4 set (Darkness bit)
Upon those conditions, it counters with an evolution... Anything else is cancelled.
Either that, or the battle uses different code than regular ones (which I think is what happens).

Hacking the game, I just found something funny... I put the Darkness bit to Meteo, and when Golbez cast it, Zeromus replied "You, the man of darkness....". So this version of Zeromus was sensitive to the darkness bit. And when I changed the spell subroutine the Crystal uses (by default, it is set to "Heal Statuses"), it doesn't matter when Cecil uses it - Zeromus still changes.