Have you checked the SH3Cmdr FAQ, specifically:
Quote:
Q: Since using SH3 Commander I can no longer hear speech or most sound effects. What sound files does SH3 Commander overwrite?
A: SH3 Commander does not overwrite any game sound files. This problem will occur if you set the "Character animations", "Sound effects" and/or "Particle rendering" Time Compression events to 1. Reset each event back to the default value and try again (a Rollback is not sufficient to reset these settings). If your problem persists, scrutinise any new mods that you have installed since you last had full sound.
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Sounds like it might not be relevant, but just to at least cross it off the list though...