As a devoted Ubuntu user, I always tell the skeptics that in Windows or Mac OS, I have to pay money for my operating system and applications, then I have to do their beta testing for them. In Ubuntu, if you can fix it — it is yours with no need to pull out the credit card.
I was challenged when I upgraded from Ubuntu Gutsy 8.10 to Jaunty 9.04 in May 2009, because my trusty M_Audio Delta 44 sound cards refused to make any sound except in the Audacity application. I went into “Tech Mode” and started checking out the Ubuntu Forum. I found some confirmation that I was not alone in this post HOWTO: PulseAudio Fixes & System-Wide Equalizer Support. I also found a lot of information on ALSA here.