Yeah, had the same problem with Final Fantasy 3. Strange thing is that it sounded good with 0.390 but doesn't with 0.391 and 0.392. And I love the soundtrack.
Tried your settings, but it just improved the sound a little bit. I still use 0.390, even if it sometimes refuses to save state. Oh well.
Just for curiosity. Which batteries do you guys use? (2500, 2800, 2300?) I read a topic where a dude said Super Mario All Stars didn't work with his 2800 batteries, but then it worked when he used normal ones. That's messed up.