Here's your fix - (considering I too had the exact same problem) - what I ended up doing was installing an older version of ePSXe on my system (v1.5.2 to be more exact). I first made a save state in 1.6.0 right before the glitch occurs. I then loaded that save state in 1.5.2, put up with some delayed video and made another save state a little bit after the glitch and resumed playing in 1.6.0. It worked just as planned. It's a little bit of a hassle but too my memory that's the only glitch I encountered in the entire game anyways.
So...
1) Install ePSXe 1.5.2 (and make sure you're using 1.6.0 already)
2) In 1.6.0 make a save state shortly before the glitch in the FMV occurs. You can do this by pressing escape to exit the screen and going "RUN > SAVESTATE (F1) > SLOT 1" in the ePSXe window.
3) Load this save state (you may have to move it to the folder of ePSXe 1.5.2) and MAKE SURE you're running FF9 in ePSXE 1.5.2.
4) Wait out some slow FMV and make another save state in the same fashion as before after the glitch point passes.
5) Move the newly made save state BACK to the 1.6.0 folder
6) Load it back up in 1.6.0 - now AHEAD of the glitch - and walla!
Hopefully that works for you...