I have tried the game using VGS 1.41, and didn't seem to have any problem. But then, I just played it only for a couple of hours. The only thing I can assure you is the intro and the beginning of the game run ok without any problem. What version of VGS did you use? Did you try VGS 1.41? Hope that would help.
Yes, I have patched the VGS with psytech ff9fix5 (did I spell it correctly?) and the games.txt. But I didn't use the iso of the game. I just play it directly from the CD. Sorry for not being specific, but there's too many patches I've used. But I'm sure both of the patches mentioned have been applied. How about give it a try?
i've tried playing with the cd instead of the iso and it works great. But i realy want to play with an iso cause it seems faster and fluid.
Do you still have the game? Can you try making an iso and try it on vgs?