Nah, it worked flawlessly the whole way through. I always use ZSNES too, I was under the impression it was the standard.
That was really good and filled in an important chapter to the story. Because I was never sure how much longer the story was going to be, I trying to be really conservative with my items; I finished with both elixirs unused.
If I recall correctly, wasn't there a bit more before the actual fall that happened "off camera?" Schala was forced to send Chrono & company back through the portal, and then seal it; they of course came back later, but any plays to tell the rest of that angle?