I know how to fix it. I don't know exactly what causes it but its a bug in that FMV. You need to hit F12 in normal mode - maybe just as you save Rinoa in space. A console-ish display should appear. Then hit F8 to turn off movies. That *should* do the trick, but if you want to be extra safe, hit F9 and F11 to turn off actors and backgrounds. Then just turn them all back on when you're inside the Ragnarok and hit F12 to remove the console.
Good luck with the Propagators
, hehe