Just in case you're still around...
I don't recall any such problems from anybody else. I've certainly never encountered it. If you happen to have other hardware (such as another speaker set, another sound card you happen to have lying around or access to another computer), you could try to play a couple battles with that to see if it's something wrong with what you have.
You may have some success with upgrading or downgrading your sound drivers, if possible.
I'd also try to run with the volume set really really low in the in-game sound options (as in, that you can only just hear anything out of your speakers). Perhaps it's not really a game sound after all, but some Windows warning sound when it's trying to do something related to playing the sounds. If it still comes out in the same volume as before, it's a sign that it's not played directly in the game (while the opposite is true if it comes out low).
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