After somewhat extensive Google searching on the issue, I, as of right now, have not found a solution. I switched to the pSX emulator recently, and everything (so far) runs smoothly other than the sound. For example, at the default sound settings, scrolling through a menu in Vanilla PSX FFT produces a distorted version of the clicking sound it is meant to play. Background music isn't really affected unless I change the sound settings from what they are by default. As I'm relatively new to this emulator, any information would be helpful. Thanks!
Edit: Maybe not the best place to post, but I'm new here and unfamiliar with the topic trees.
Honestly, there's not a single emulator that handles FFT's audio properly, not even with plugins. You're not wrong, though, and you aren't alone. It's just broken.
Seems about right, I was able to mess around with the settings enough to make it almost the way it should be when I got the chance to. It's the best it'll get, won't be the end of the world.