Alsa needs reconfiguration after every reboot
Are you using Sarge or Etch?
It sounds like you have a problem with your install. You only need to run alasaconf once and it saves the configuration. After that you only need to run alsaconf if you change your sound card or add one.
Try using apt-get to purge alsa-base and alsa-utils. Clear apt-get's cache. Update apt-get then install alsa-base. Run alsaconf then reboot to see if the problem is fixed. If this does not work I recommend doing a clean install.
I've been using Etch and upgrading as the repository changes and have had some strange problems crop up. The only thing that fixed them was a clean re-install of Etch.