....and a third possibility.....and the most likely, is that the digital signal sent over s/pdif is not bit-perfect from the source file.
As has been mentioned, Windows XP sound drivers ...kmixer will take a stereo pcm signal at 44.1khz, and do a really lousy resample to 48 khz (and I think back again to 44.1khz).
The result is a very clear noticeable degradation....even untrained ears can pick it out quickly.
Very few sound cards, and almost no motherboard audio chipsets support bypassing this kmixer driver UNDER WINDOWS XP.
I believe that Vista/7 makes this a non-issue either by passing bitperfect, or having a far better resample algorithm. So s/pdif output from motherboard audio or all soundcards should rival the s/pdif output of a cd player (and the difference here will probably be due to jitter....and I do not know how significant jitter degredation can be).
Edit......oops. ....never mind. Looks like you are saying same thing with HDCD test....
Wish there was a simpler way to verify bitperfect output.