I’m looking forward to your update, and to hear whether my suggestion in #48 helped out. What you’re describing sounds like “phase cancellation” (google that term) — either because the speakers are wired incorrectly (likely) or because one channel of the audio file has been inverted or shifted very slightly (very unusual).
This article explains the phenomenon a bit:
http://www.audiocourses.com/article1664.html
Huh... If that was the case, then why would I still be successfully loading other CDs from other artists, and why would the other 80 bajillion songs I have already loaded over the years still sound great, just as they have for all the years that I've used this (totally untinkered-with) computer?