In Mario & Luigi (the 1st one), one of the sound channels keeps going in/out during gameplay (eg: the sound of coins collected after battle may go missing). I've tried more or less every combination of sound option, and haven't been able to isolate the issue. Tested with/without BIOS, just to ensure that wasn't a problem.
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I know a late build of VBA-S had the same issue, so I guess its been around for a while...could just be that game though. I should note, the last time I used VBA-S was on an older PC, so that mostly rules out a hardware issue.
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As of now, I have not noticed this behavior in any other game...
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EDIT
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Forgot to mention, using the latest (Nov 10) SVN. Also should note, my current soundcard is an ASUS Xonar D2 (though my Realtek controler has the same problem in this game...)