What's the Audio interface? Does it use drivers?
I have an Edirol FA-66, and have no problem maintaining setting between reboots.
Having said that, there do seem to be a lot of people posting at the moment with problems about System Preferences not being retained. Might be worth following a few similar threads.
You can always go to the <user>/Library/Preferences folder, sort it by Modification Date, change a preference, see what files get changed, and then open them in a text editor like TextWrangler, which automatically decodes plist files. Then you can see if the preference value is being saved, and investigate the file after reboot.
Note that "a bug" and "a problem on your computer" are two different things!