Dang it! I knew I forgot something! It's caused by the bugfix (Gerad and Sabin) for that moment in the script. If any editing is done in FF3USME, then it messes with that bugfix. For some reason, ANY of Leet Sketcher's fixes have an issue with TWUE if you use FF3USME to edit after the fact. I'm going to fix it soon (give me a day or so!)
However, if you want to fix it yourself, download Leet Sketcher's fix here: http://www.romhacking.net/hacks/2650/ and use the unheadered reverse patch, then repatch it with the unheadered fix.
Thanks man. So far I've been able to continue with the game without any issues after loading the save state in a vanilla ROM, getting past that, and then loading the original ROM. I should note I'm using the TWUE with all of the options selected.