Hi,
Thanks for the code snippets and link.
The root reason for the stuttering is the ring buffer used by FMOD to output sound is not getting any new data so it will continue to play what is still in the buffer, as it is very small it sounds very harsh.
While this seems to solve the issue it only delays the time till you experience a stutter.
We recently created a Unity example using FMOD as the audio output which can be found here: Is Unity's built-in audio engine FMOD Studio (FMOD 5)? - #10 by jeff_fmod.
Hope this helps!