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After my recent sound stutter problem with P4(which is yet unsolved) I decided to test on other games to see if they have the same problem-which they did. Both Mana Khemia 2 and Megaman X command mission have the same problem of getting sound stutter when saving games on their respective save menus and occasional minor stutter in-game. The problem is with sound only,the fps was running 59-60 fine when stutter happens and I didn't enable any speedhacks.

Persona 3 at least runs a lot of IOP code while streaming music. This leads to sound issues due to bad processor synchronization.
Try using the EE cycle speedhacks and see if that fixes the problem.

Um..I was running Persona 4,not 3. Did as you suggested,adjusting EE from 1-3 and it's still the same. Minor sound stutters occurred whenever I saved games.