When I updated to ubuntu 10.10, I had this mysterious problem.
The sub-woofer just worked one time right after I clicked the "5.1 System" in the ubuntu sound options. As soon as a song ended, the sub-woofer was mute again.
I expected this to be an issue of the pulseaudio integration in 10.10. The reason was way simpler!
In 10.10 by default:
enable-lfe-remixing = no
is set in
Just change this to
enable-lfe-remixing = yes
and pulseaudio will mix the 2 channel sound tracks up to the 5 channels including LFE!