If you're using ALSA, I belive you can turn it down using alsamixer.
I am using ALSA on the default kernel (for slackware) and ALSA does not change the volume of the system beep.
It is a kernel thing, if you want to disable it altogether, it's either disabled by the kernel or by unplugging it.
Again, muting it in ALSAmixer might work, but it's been my experience that it doesn't.
-Jason
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