Motherboard volume TOO loud

Hello, my computer makes an odd and loud sound while running "certain"
applications. I am almost sure that it is the motherboard speaker. I looked
in the BIOS menu but couldn't find any type of control. If I lower the
master volume within the Windows mixer and do certain events, the sound is
heard again quite loud, if I mute the device (or master volume) then the
sound finally is shut.

Is there any way to configure the the volume speaker through any sort
of application or trick? I guess somehow the mixer is not watching the extra
device (motherboard speaker) or my application.

By the way, I muted the application and the sound after the event
persists.