make sure your Fedora installation isn't loading the "pcspkr" module.
pcspkr is a module that interfaces to the cheap motherboard 'beep' speaker (you are hearing the beep from the motherboard and not from the audio speakers right?). You can completely stop it from loading in any case by blacklisting it:
as the root user, edit the file /etc/modprobe.d/blacklist.conf to add these lines:
alias pcspkr /bin/true
with that saved, now make sure there's no loaded pcspkr module
The tone speaker on the board should be disabled in Fedora now