Well, I figured out my problem regarding why music kept fading in and out... Apparently SuperCDs require the extra memory of the Duo to play music properly. I first tried a HuCard, which played fine, and then the intro to Y's (regular CD) played fine. When I went to play the game, however, I received a message that "Internal memory is not initialized". I reset the system and formatted the memory, and now everything plays fine (Lords of Thunder, Gate of Thunder, Super Air Zonk, Dracula X, etc.).
I guess since I hadn't played the Duo in some time that the memory reset/corrupted itself? Whatever. Anyway, it works now. Hopefully if anyone else is having this same problem it will be a good FYI.