I think I found the issue. This one script file is a special snowflake in that the dialogue for that sequence would be bigger than the the space allowed for a text sequence. The Max size is 0xFFF and this would be over that. So Sony split it up and moved it around to another sequence that had space for it. As a result my portrait corrector code that I wrote to correct portraits in a few spots where the PS1 version rearranged them got thrown for a loop and screwed everything up.
That said I believe I have it fixed with the attached patch. This should fix the portraits and also includes above updates to the Map Screens and Battle Results screens. I've only tested a few of the maps on real hardware so let me know if any act up.
Also with the news that disc 1 can be completed, I'm going to start focusing on trying to clean up the out of sync audio for the rest of disc 1 as well as any remaining uncompressed graphical text. Once that is done all that should remain is the compressed battle graphics, the FMVs, and the few sequences that are voiced with no text. At that point I'll begin shifting focus to Disc 2.