Flare consumes all your MP, and it also has a minimum cost. It's something like 266 at Lv50; I don't recall the exact values for other levels. So if you cast too many spells and get below that, Flare is no longer and option. You can see the minimum cost if you drop below it and check the tooltip again--the easiest way to do this is to Flare and then check while you're still in Astral Fire and not refreshing MP.
Prior to getting the Umbral Heart discount for Flare, the AoE rotation looks something like this:
Fire III
Fire II
Fire II
Fire II* (only if you have enough MP to use it and still Flare; you prolly won't)
Flare
Transpose
Thunder II
Repeat from Fire III
Don't bother using a GCD on Blizzard III; you want to get back into Fire ASAP. You also might not be at full MP, and that's okay. Between the cast times of Thunder II and Fire III, you should have enough MP for Fire II, Fire II, Flare.