Comment 5 for bug 398161

rmmod followed by modprobe seems to be the only way it works for me. I only reboot for distribution upgrades and (sometimes) hardware updates, so it's often a couple months since I rebooted and I forget to do this. So it's kind of a problem for me, because I use system beep for my alarm clock. I've now tried adding this to /etc/rc.local:

rmmod pcspkr || true
modprobe pcspkr || true
rmmod pcspkr || true
modprobe pcspkr || true

(twice just in case that's necessary) and made sure it's executable. I guess I'll see if that works next time I reboot.