I have this EXACT same problem. At the spot where Zidane goes: Well here I go (or something just like that), after everyone else leaves.
I use Pete's DirectX 7 plugin., also Null2's, WITH linear interpolation (it sounds a whole bunch better). ummm
Basically, everything else is the same...uhh, including the bios. have you tried with 7502?
I have found that the null2 is a LOT better for FF9 (for me). I would hate to have to use the internal SPU for the ending...but if I absolutely have to, I guess I will. So...do I have to?
Otherwise, th only other problem I have with FF9 is on entering battles, it keeps swirling instead of going to black, and so I guess the music slows down.