well, are you playing the game from an ISO or from the CD itself? naturally, the CD will cause lagg, I highly Advise you Rip the Disk first to an iso and play it on the PC, you'll get faster load times and sound will be less choppy.
you may also wanna check the forums 'search' for configs and TIPS for configurations for FF9 [ I remember seeing quite a number for ff9]
oops, here check this page >>
LINK
Goodluck
CHeers
-Leerz