Comment 19 for bug 388547

There is a workaround for this. I used to use this on Debian with a small set of packages.

Using acpid and amixer one can set an acpid rule to react at volume keys at a deeper level than the default sound daemon.
Use acpi_listen to discover your key codes and write a script like this (for example when pressing volume up):
amixer set Master 5+
This is more ALSA related, but pulseaudio will adjust its volume as well.