Sound issues with Final Fantasy 6 Advance

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What steps will reproduce the problem?
1. Play through till Terra faints after falling into a cave (scene seconds 
before you gain control of Locke and moogles), during the flashback with kefka 
the sound is quite slow (framerate seems to be as well, but the framerate 
counter never drops below 55).
2. Sound issues intermixed during gameplay, no real noticeable reason or rhyme.

What is the expected output? What do you see instead?
See above.

What version of the product are you using? On what operating system?
VBA-PS3-0.9.9.1 on firmware 3.41

Original issue reported on code.google.com by sakananokami@gmail.com on 8 Dec 2010 at 9:54

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Side note: This also is being played as a .gba as opposed to a .zip and from 
the internal hard drive, not external.  Filter is stock, tried with a GBA bios 
and without, also tried with 480p resolution as opposed to 1080p.

Original comment by sakananokami@gmail.com on 8 Dec 2010 at 9:58

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Just trying to give more info.  The sound seems to be fine in the options menu, 
it's when in actual gameplay, and after playing a bit more it seems to be 
everywhere otherwise, in battles, walking around, etc.  The gameplay appears to 
run fine.  Also noticed the game slowed down a bit when a lot of animation 
occurred on screen (ie: Doing one of the more flashy spells), in both sound and 
gameplay.  Nothing overly huge, but definitely noticeable.

Original comment by sakananokami@gmail.com on 12 Dec 2010 at 1:24

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Updated to version 1.01, all others remain the same.  Many frame rate issues 
seem to be fixed.  Still a few speed issues, most noticeable was during areas 
riding a chocobo.  Frame rate still doesn't drop below 50-55, but it is enough 
that the sound stutters and the game runs visibly slower. But a step in the 
right direction indeed!

Original comment by sakananokami@gmail.com on 16 Jan 2011 at 3:30