Wanted to give you all the info I had on it. I know I had the frozen flames from before fighting through the omen at all. I also never beat lavos from the Omen, instead leaving after the queen fight each time, that's how I got 3 prizm dresses, and 6 prizm helms without a new game plus. So at my save file, you can no longer go to the omen at all, since all three available have been destroyed. 1000, 600, and 12000. So the error I got happens when I try to beat the game (for the first time) from the bucket, as there are only 2 ways to lavos at that point. the bucket, or epoch (which I believe are really the same event). I say try, because you end up fighting the outside of lavos, and then the game starts the new ending in Zeal. If magus is in the finishing party at that point, it starts the prophets guile cut scene (I think), and then bugs out. If hes NOT in the party, the ending works properly, but then doesn't end the game with the book, and instead sends you to cronos moms room (unless that is intended), and there is no way to get the game to be completed, and no credits, or new game plus. You can then do the same outer lavos fight from the bucket over and over, getting the zeal ending each time but just ending up back in cronos moms room, with now way to close out the game. Again, some of this may be completely intended, so I may be wrong in whats supposed to happen. Anyway, I do wish you luck in figuring this out, and will provide any more info you need if I can.
Oh, one more thing, I got and used all the chips (except from the thunder dome), I did it once thinking I could try again, not realizing its a one and done thing.
If the issues stem from the frozen flame(s), then I should try to play through again trying to see where I first picked them up. I have another save file from much earlier in the game, I can use to see where they may have come from. If that would be helpful, I can try.