Alright, I'm by no means an expert on any of this but I spent a lot of time trying to fix the freeze, so here is my experience. The first time I ran into this was the giant of babil cutscene. No big deal, tried it again, just fine. Then once going to and from the moon (yeah, make sure you save every time before you do this), which confirmed for me it was the cutscenes. I beat the game and it froze on the first ending cutscene (yes sadly there are two), reloaded and it was fine. Beat it again with different characters, just fine. Needed one last character's seal unlocked for the bonus dungeon, and it froze randomly on either cutscene on NINETEEN ATTEMPTS. it's a good thing I love this game or would I have given up. In those 19 attempts I tried both releases, CSOs, compressing myself, fiddled with the clock speed and every combination of firmware settings I could possibly imagine... It doesn't matter, it's either AP or some weird incompatibility with 5.50 prom 4. I'm betting the former.
Deleting or dummying the movies doesn't work, it won't just skip them. What I did to get around the ending finally was replacing the two ending movies, END.pmf and Misidia.pmf, with ZOT.pmf. This will drastically reduce the odds of a freeze, as Zot is only about two seconds long and the other two are much, much longer. It isn't an elegant solution, as the sound will be out of sync for the whole ending and the text crawl for the legend will run over the actual in game ending stuff, but at least you can get through it all the way.
Deleting or dummying the movies doesn't work, it won't just skip them. What I did to get around the ending finally was replacing the two ending movies, END.pmf and Misidia.pmf, with ZOT.pmf. This will drastically reduce the odds of a freeze, as Zot is only about two seconds long and the other two are much, much longer. It isn't an elegant solution, as the sound will be out of sync for the whole ending and the text crawl for the legend will run over the actual in game ending stuff, but at least you can get through it all the way.